Zymo_Mock_HMW_SUP_duplex_reads_with_peregrine_2021

gistfile1.txt

This was with https://zymo-files.s3.amazonaws.com/BioPool/ZymoBIOMICS.STD.refseq.v2.zip

RAW_SUP_Duplex                                         pg_asm_1x_corrected_SUP_duplex                         pg_asm_2x_corrected_SUP_duplex                         pg_asm_3x_corrected_SUP_duplex
Bacillus_subtilis                                      Bacillus_subtilis                                      Bacillus_subtilis                                      Bacillus_subtilis
# target bases: 4041255                                # target bases: 4041255                                # target bases: 4041255                                # target bases: 4041255
# target bases overlapping regions: 4041255 (100.00%)  # target bases overlapping regions: 4041255 (100.00%)  # target bases overlapping regions: 4041255 (100.00%)  # target bases overlapping regions: 4041255 (100.00%)
1159311 reference bases covered by exactly one contig  3791080 reference bases covered by exactly one contig  3642732 reference bases covered by exactly one contig  3786472 reference bases covered by exactly one contig
26 substitutions; ts/tv = 1.889                        18 substitutions; ts/tv = 2.600                        18 substitutions; ts/tv = 2.600                        17 substitutions; ts/tv = 2.400
20 1bp deletions                                       3 1bp deletions                                        4 1bp deletions                                        4 1bp deletions
5 1bp insertions                                       1 1bp insertions                                       1 1bp insertions                                       1 1bp insertions
1 2bp deletions                                        0 2bp deletions                                        0 2bp deletions                                        0 2bp deletions
0 2bp insertions                                       0 2bp insertions                                       0 2bp insertions                                       0 2bp insertions
0 [3,50) deletions                                     0 [3,50) deletions                                     0 [3,50) deletions                                     0 [3,50) deletions
0 [3,50) insertions                                    0 [3,50) insertions                                    0 [3,50) insertions                                    0 [3,50) insertions
0 [50,1000) deletions                                  0 [50,1000) deletions                                  0 [50,1000) deletions                                  0 [50,1000) deletions
0 [50,1000) insertions                                 1 [50,1000) insertions                                 1 [50,1000) insertions                                 1 [50,1000) insertions
0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions
0 >=1000 insertions                                    2 >=1000 insertions                                    2 >=1000 insertions                                    2 >=1000 insertions
# samtools stats read alignment (map Qual=60) error rate
1.300449e-03                                           7.950136e-04                                           7.869161e-04                                           7.867193e-04

### This reference is from ATCC genomes
Enterococcus_faecalis                                  Enterococcus_faecalis                                  Enterococcus_faecalis                                  Enterococcus_faecalis
# target bases: 2790314                                # target bases: 2790314                                # target bases: 2790314                                # target bases: 2790314
# target bases overlapping regions: 2526050 (90.53%)   # target bases overlapping regions: 2526050 (90.53%)   # target bases overlapping regions: 2526050 (90.53%)   # target bases overlapping regions: 2526050 (90.53%)
325487 reference bases covered by exactly one contig   1243807 reference bases covered by exactly one contig  1327819 reference bases covered by exactly one contig  1335426 reference bases covered by exactly one contig
2519 substitutions; ts/tv = 3.164                      9279 substitutions; ts/tv = 3.509                      9895 substitutions; ts/tv = 3.514                      9960 substitutions; ts/tv = 3.509
14 1bp deletions                                       57 1bp deletions                                       58 1bp deletions                                       58 1bp deletions
12 1bp insertions                                      53 1bp insertions                                      57 1bp insertions                                      57 1bp insertions
0 2bp deletions                                        4 2bp deletions                                        4 2bp deletions                                        4 2bp deletions
1 2bp insertions                                       2 2bp insertions                                       2 2bp insertions                                       2 2bp insertions
3 [3,50) deletions                                     11 [3,50) deletions                                    12 [3,50) deletions                                    12 [3,50) deletions
3 [3,50) insertions                                    16 [3,50) insertions                                   16 [3,50) insertions                                   16 [3,50) insertions
0 [50,1000) deletions                                  4 [50,1000) deletions                                  4 [50,1000) deletions                                  4 [50,1000) deletions
0 [50,1000) insertions                                 4 [50,1000) insertions                                 8 [50,1000) insertions                                 8 [50,1000) insertions
4 >=1000 deletions                                     10 >=1000 deletions                                    10 >=1000 deletions                                    10 >=1000 deletions
1 >=1000 insertions                                    7 >=1000 insertions                                    7 >=1000 insertions                                    7 >=1000 insertions
# samtools stats read alignment (map Qual=60) error rate
5.005881e-02                                           5.060479e-02                                           5.062398e-02                                           5.062993e-02


### This reference is from Zymo
Enterococcus_faecalis                                  Enterococcus_faecalis                                  Enterococcus_faecalis                                  Enterococcus_faecalis
1116406 reference bases covered by exactly one contig  2591694 reference bases covered by exactly one contig  2684232 reference bases covered by exactly one contig  2682675 reference bases covered by exactly one contig
18 substitutions; ts/tv = 8.000                        47 substitutions; ts/tv = 2.615                        47 substitutions; ts/tv = 2.615                        47 substitutions; ts/tv = 2.615
2 1bp deletions                                        4 1bp deletions                                        4 1bp deletions                                        4 1bp deletions
0 1bp insertions                                       5 1bp insertions                                       4 1bp insertions                                       4 1bp insertions
0 2bp deletions                                        0 2bp deletions                                        0 2bp deletions                                        0 2bp deletions
0 2bp insertions                                       1 2bp insertions                                       1 2bp insertions                                       1 2bp insertions
0 [3,50) deletions                                     0 [3,50) deletions                                     0 [3,50) deletions                                     0 [3,50) deletions
0 [3,50) insertions                                    2 [3,50) insertions                                    2 [3,50) insertions                                    2 [3,50) insertions
0 [50,1000) deletions                                  0 [50,1000) deletions                                  0 [50,1000) deletions                                  0 [50,1000) deletions
0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions
0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions
0 >=1000 insertions                                    0 >=1000 insertions                                    0 >=1000 insertions                                    0 >=1000 insertions                                    
# samtools stats read alignment (map Qual=60) error rate
8.843090e-03                                           8.610355e-03                                           8.618782e-03                                           8.617423e-03


Escherichia_coli                                       Escherichia_coli                                       Escherichia_coli                                       Escherichia_coli
# target bases: 4875441                                # target bases: 4875441                                # target bases: 4875441                                # target bases: 4875441
# target bases overlapping regions: 4875158 (99.99%)   # target bases overlapping regions: 4765089 (97.74%)   # target bases overlapping regions: 4765089 (97.74%)   # target bases overlapping regions: 4765089 (97.74%)
2583750 reference bases covered by exactly one contig  4670961 reference bases covered by exactly one contig  4670961 reference bases covered by exactly one contig  4670961 reference bases covered by exactly one contig
402 substitutions; ts/tv = 1.892                       553 substitutions; ts/tv = 1.957                       553 substitutions; ts/tv = 1.957                       553 substitutions; ts/tv = 1.957
33 1bp deletions                                       10 1bp deletions                                       10 1bp deletions                                       10 1bp deletions
16 1bp insertions                                      15 1bp insertions                                      15 1bp insertions                                      15 1bp insertions
4 2bp deletions                                        2 2bp deletions                                        2 2bp deletions                                        2 2bp deletions
3 2bp insertions                                       1 2bp insertions                                       1 2bp insertions                                       1 2bp insertions
4 [3,50) deletions                                     1 [3,50) deletions                                     1 [3,50) deletions                                     1 [3,50) deletions
2 [3,50) insertions                                    4 [3,50) insertions                                    4 [3,50) insertions                                    4 [3,50) insertions
0 [50,1000) deletions                                  1 [50,1000) deletions                                  1 [50,1000) deletions                                  1 [50,1000) deletions
0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions
0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions
1 >=1000 insertions                                    0 >=1000 insertions                                    1 >=1000 insertions                                    1 >=1000 insertions
# samtools stats read alignment (map Qual=60) error rate
1.070861e-03                                           7.181472e-04                                           7.074496e-04                                           7.071868e-04

Listeria_monocytogenes                                 Listeria_monocytogenes                                 Listeria_monocytogenes                                 Listeria_monocytogenes
# target bases: 2992056                                # target bases: 2992056                                # target bases: 2992056                                # target bases: 2992056
# target bases overlapping regions: 2992056 (100.00%)  # target bases overlapping regions: 2992056 (100.00%)  # target bases overlapping regions: 2992056 (100.00%)  # target bases overlapping regions: 2992056 (100.00%)
1326181 reference bases covered by exactly one contig  2717713 reference bases covered by exactly one contig  2766521 reference bases covered by exactly one contig  2887788 reference bases covered by exactly one contig
2 substitutions; ts/tv = 1.000                         3 substitutions; ts/tv = 2.000                         2 substitutions; ts/tv = 1.000                         3 substitutions; ts/tv = 2.000
3 1bp deletions                                        1 1bp deletions                                        0 1bp deletions                                        0 1bp deletions
1 1bp insertions                                       0 1bp insertions                                       1 1bp insertions                                       1 1bp insertions
1 2bp deletions                                        0 2bp deletions                                        0 2bp deletions                                        0 2bp deletions
0 2bp insertions                                       0 2bp insertions                                       0 2bp insertions                                       0 2bp insertions
0 [3,50) deletions                                     0 [3,50) deletions                                     0 [3,50) deletions                                     0 [3,50) deletions
0 [3,50) insertions                                    0 [3,50) insertions                                    0 [3,50) insertions                                    0 [3,50) insertions
0 [50,1000) deletions                                  0 [50,1000) deletions                                  0 [50,1000) deletions                                  0 [50,1000) deletions
0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions
0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions
0 >=1000 insertions                                    0 >=1000 insertions                                    0 >=1000 insertions                                    0 >=1000 insertions
# samtools stats read alignment (map Qual=60) error rate
4.337566e-04                                           1.859414e-05                                           1.089206e-05                                           1.021797e-05

### Something is strange about this reference direct from Zymo?
Saccharomyces_cerevisiae                               Saccharomyces_cerevisiae                               Saccharomyces_cerevisiae                               Saccharomyces_cerevisiae
# target bases: 12225336                               # target bases: 12225336                               # target bases: 12225336                               # target bases: 12225336
# target bases overlapping regions: 3126602 (25.57%)   # target bases overlapping regions: 6597540 (53.97%)   # target bases overlapping regions: 7581784 (62.02%)   # target bases overlapping regions: 6958316 (56.92%)
2317190 reference bases covered by exactly one contig  5541039 reference bases covered by exactly one contig  5998900 reference bases covered by exactly one contig  6117162 reference bases covered by exactly one contig
3207 substitutions; ts/tv = 2.742                      5539 substitutions; ts/tv = 2.678                      5729 substitutions; ts/tv = 2.767                      6729 substitutions; ts/tv = 2.836
299 1bp deletions                                      394 1bp deletions                                      410 1bp deletions                                      450 1bp deletions
244 1bp insertions                                     355 1bp insertions                                     403 1bp insertions                                     467 1bp insertions
71 2bp deletions                                       98 2bp deletions                                       94 2bp deletions                                       121 2bp deletions
55 2bp insertions                                      104 2bp insertions                                     108 2bp insertions                                     114 2bp insertions
75 [3,50) deletions                                    103 [3,50) deletions                                   121 [3,50) deletions                                   114 [3,50) deletions
54 [3,50) insertions                                   136 [3,50) insertions                                  135 [3,50) insertions                                  150 [3,50) insertions
2 [50,1000) deletions                                  7 [50,1000) deletions                                  8 [50,1000) deletions                                  11 [50,1000) deletions
5 [50,1000) insertions                                 12 [50,1000) insertions                                11 [50,1000) insertions                                12 [50,1000) insertions
0 >=1000 deletions                                     1 >=1000 deletions                                     2 >=1000 deletions                                     2 >=1000 deletions
0 >=1000 insertions                                    2 >=1000 insertions                                    3 >=1000 insertions                                    8 >=1000 insertions
# samtools stats read alignment (map Qual=60) error rate
1.113377e-02                                           1.033118e-02                                           1.019597e-02                                           1.016335e-02

Salmonella_enterica                                    Salmonella_enterica                                    Salmonella_enterica                                    Salmonella_enterica
# target bases: 4809318                                # target bases: 4809318                                # target bases: 4809318                                # target bases: 4809318
# target bases overlapping regions: 4806012 (99.93%)   # target bases overlapping regions: 4756440 (98.90%)   # target bases overlapping regions: 4806012 (99.93%)   # target bases overlapping regions: 4806012 (99.93%)
1186015 reference bases covered by exactly one contig  2021577 reference bases covered by exactly one contig  2855944 reference bases covered by exactly one contig  3301669 reference bases covered by exactly one contig
76 substitutions; ts/tv = 1.714                        26 substitutions; ts/tv = 5.500                        24 substitutions; ts/tv = 3.000                        32 substitutions; ts/tv = 2.556
53 1bp deletions                                       3 1bp deletions                                        3 1bp deletions                                        4 1bp deletions
50 1bp insertions                                      8 1bp insertions                                       12 1bp insertions                                      10 1bp insertions
6 2bp deletions                                        1 2bp deletions                                        0 2bp deletions                                        0 2bp deletions
2 2bp insertions                                       0 2bp insertions                                       2 2bp insertions                                       2 2bp insertions
4 [3,50) deletions                                     0 [3,50) deletions                                     1 [3,50) deletions                                     0 [3,50) deletions
2 [3,50) insertions                                    0 [3,50) insertions                                    0 [3,50) insertions                                    1 [3,50) insertions
0 [50,1000) deletions                                  0 [50,1000) deletions                                  0 [50,1000) deletions                                  0 [50,1000) deletions
0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions
0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions
0 >=1000 insertions                                    0 >=1000 insertions                                    0 >=1000 insertions                                    0 >=1000 insertions
# samtools stats read alignment (map Qual=60) error rate
1.193091e-03                                           7.012235e-04                                           6.661453e-04                                           6.602791e-04

Staphylococcus_aureus                                  Staphylococcus_aureus                                  Staphylococcus_aureus                                  Staphylococcus_aureus
# target bases: 2730326                                # target bases: 2730326                                # target bases: 2730326                                # target bases: 2730326
# target bases overlapping regions: 2721773 (99.69%)   # target bases overlapping regions: 2718780 (99.58%)   # target bases overlapping regions: 2725117 (99.81%)   # target bases overlapping regions: 2725117 (99.81%)
2245965 reference bases covered by exactly one contig  2646579 reference bases covered by exactly one contig  2646408 reference bases covered by exactly one contig  2646412 reference bases covered by exactly one contig
11 substitutions; ts/tv = 1.750                        12 substitutions; ts/tv = 2.000                        12 substitutions; ts/tv = 2.000                        12 substitutions; ts/tv = 2.000
8 1bp deletions                                        7 1bp deletions                                        7 1bp deletions                                        7 1bp deletions
1 1bp insertions                                       1 1bp insertions                                       1 1bp insertions                                       1 1bp insertions
1 2bp deletions                                        1 2bp deletions                                        1 2bp deletions                                        1 2bp deletions
2 2bp insertions                                       2 2bp insertions                                       2 2bp insertions                                       2 2bp insertions
1 [3,50) deletions                                     1 [3,50) deletions                                     1 [3,50) deletions                                     1 [3,50) deletions
1 [3,50) insertions                                    1 [3,50) insertions                                    1 [3,50) insertions                                    1 [3,50) insertions
1 [50,1000) deletions                                  1 [50,1000) deletions                                  1 [50,1000) deletions                                  1 [50,1000) deletions
0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions                                 0 [50,1000) insertions
0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions                                     0 >=1000 deletions
0 >=1000 insertions                                    0 >=1000 insertions                                    0 >=1000 insertions                                    0 >=1000 insertions
# samtools stats read alignment (map Qual=60) error rate
4.146390e-04                                           5.414635e-05                                           4.700935e-05                                           4.653782e-05