Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A2 F5 I178 R1
|
167 |
28.0 |
1137820 |
95.3% |
1084342 |
115.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
489,334 |
T→G |
V596G (GTG→GGG) |
dnaX → |
DNA polymerase III subunit gamma/tau |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 489,334 | 0 | T | G | 95.5%
| 72.6
/ ‑3.2
| 22 | V596G (GTG→GGG) | dnaX | DNA polymerase III subunit gamma/tau |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (9/12); total (9/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01 |
GTATGTCTGCATTTGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGTGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATGAAGAAAGTATCCG > NZ_CP009273/489201‑489469
|
gTATGTCTGCATTTGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTa < 1:348116/139‑1 (MQ=255)
tGTCTGCATTTGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTAcgc > 2:77410/1‑139 (MQ=255)
tttGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAg > 2:462313/1‑139 (MQ=255)
aGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGat < 1:77410/139‑1 (MQ=255)
aGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGa > 1:467092/1‑138 (MQ=255)
cATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATAc > 2:224410/1‑138 (MQ=255)
cATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATAc > 1:409627/1‑138 (MQ=255)
tttGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCAGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACg > 1:230202/1‑137 (MQ=255)
aGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGgcgcg < 1:224410/139‑1 (MQ=255)
aaaaaCTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGa < 2:74704/139‑1 (MQ=255)
aaGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTg < 2:122208/138‑1 (MQ=255)
aGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGTGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCg < 1:283719/139‑1 (MQ=255)
aGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCg < 2:391174/139‑1 (MQ=255)
cGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGa < 2:559624/139‑1 (MQ=255)
aaGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGAc > 2:364154/1‑139 (MQ=255)
tCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGc > 2:534650/1‑139 (MQ=255)
aaCGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGt < 1:546069/139‑1 (MQ=255)
aCTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATg > 2:274564/1‑139 (MQ=255)
gatgatAATCCCGCAGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATg < 2:230202/139‑1 (MQ=255)
tAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATgaagaa < 1:534650/139‑1 (MQ=255)
cgGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATGAAGAAAGTATCCg < 1:274564/139‑1 (MQ=255)
cgGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATGAAGAAAGTATCCg < 2:76087/139‑1 (MQ=255)
|
GTATGTCTGCATTTGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGTGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATGAAGAAAGTATCCG > NZ_CP009273/489201‑489469
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AACGCAGTATGTCTGCATTTGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGTGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATGAAGAAAGTATCCGCCCCATTTGAT > NZ_CP009273/489195‑489480
|
agacagGTATGTCTGCATTTGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGC < SRR3722132.204287/145‑1 (MQ=60)
AGTATGTCTGCATTTGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAG < SRR3722132.354564/151‑1 (MQ=60)
GCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGAT > SRR3722132.475459/1‑150 (MQ=60)
CCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACG > SRR3722132.417068/1‑150 (MQ=60)
TCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCAGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGA > SRR3722132.234518/1‑149 (MQ=60)
CAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAA < SRR3722132.78815/151‑1 (MQ=60)
CAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTA < SRR3722132.228608/151‑1 (MQ=60)
AAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGTGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATAT < SRR3722132.289111/151‑1 (MQ=60)
CAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGA < SRR3722132.555675/151‑1 (MQ=60)
ATAATCCCGCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATGAAGAAAGTATCCGCCC < SRR3722132.544102/151‑1 (MQ=60)
GCGGGGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATGAAGAAAGTATCCGCCCCATTTGAT < SRR3722132.279794/151‑1 (MQ=60)
|
AACGCAGTATGTCTGCATTTGCGCTCCTCTCAGCGGCATTTGAACAACCGCGGTGCACAGCAAAAACTGGCTGAAGCGTTGAGCATGTTAAAAGGTTCAACGGTTGAACTGACTATCGTTGAAGATGATAATCCCGCGGTGCGTACGCCGCTGGAGTGGCGTCAGGCGATATACGAAGAAAAACTTGCGCAGGCGCGCGAGTCCATTATTGCGGATAATAATATTCAGACCCTGCGTCGGTTCTTCGATGCGGAGCTGGATGAAGAAAGTATCCGCCCCATTTGAT > NZ_CP009273/489195‑489480
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
