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 |
|
A1 F2 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,795,564 |
T→A |
T422S (ACT→TCT) |
thrS ← |
threonine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,795,564 | 0 | T | A | 96.0%
| 87.1
/ ‑3.3
| 25 | T422S (ACT→TCT) | thrS | threonine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base A (8/16); total (8/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.68e-01 |
GATGTTGTTTTCTTCCAGCGCAACCGCCAGGTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGTGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGACTAAACGGATACATC > NZ_CP009273/1795478‑1795632
|
gATGTTGTTTTCTTCCAGCGCAACCGCCAGGTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGga > 2:646287/1‑90 (MQ=255)
ttcttcCAGCGCAACCGCCAGGTCCGCCTCAGCACGATCCCACA‑‑TCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTgacga > 2:299977/1‑90 (MQ=255)
tcCAGCGCAACCGCCAGGTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGacgacg > 2:839378/1‑90 (MQ=255)
gCCAGGTCCGCCTCAGCACGAGCCCACATTTCGTCGCTTCCAATACGTTTTTCAGGACGAGTGGAGAGTTTGACGACGATCTTCTCGAAg < 2:869826/90‑1 (MQ=255)
cAGGTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGcc < 2:473085/90‑1 (MQ=255)
gTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCaaa < 1:637677/90‑1 (MQ=255)
gTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCaaa < 2:63365/90‑1 (MQ=255)
gTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCaaa < 1:675814/90‑1 (MQ=255)
ccTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGc < 2:623580/90‑1 (MQ=255)
tCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTg < 2:195094/90‑1 (MQ=255)
tCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTg < 1:86283/90‑1 (MQ=255)
tCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTg < 2:514432/90‑1 (MQ=255)
tCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTg < 2:110922/90‑1 (MQ=255)
tCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTg < 1:810252/90‑1 (MQ=255)
tCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTg < 1:697269/90‑1 (MQ=255)
cACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACa < 1:839378/90‑1 (MQ=255)
aTCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTg < 1:278059/82‑1 (MQ=255)
aTCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTg > 2:278059/1‑82 (MQ=255)
tCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCa < 2:362342/90‑1 (MQ=255)
tcgtcgCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGACTaaa > 2:539257/1‑90 (MQ=255)
tcgtcgCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGACTaaa > 2:801211/1‑90 (MQ=255)
tcgtcgCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGACTaaa > 2:570030/1‑90 (MQ=255)
tcgtcgCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGACTaaa > 2:139066/1‑90 (MQ=255)
tGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGACTAAACGGATAc < 2:791335/90‑1 (MQ=255)
cAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGACTAAACGGATACATc < 2:304995/90‑1 (MQ=255)
|
GATGTTGTTTTCTTCCAGCGCAACCGCCAGGTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGTGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGACTAAACGGATACATC > NZ_CP009273/1795478‑1795632
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAAACGGGATGTTGTTTTCTTCCAGCGCAACCGCCAGGTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGTGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGAC > NZ_CP009273/1795471‑1795618
|
CAAACGGGATGTTGTTTTCTTCCAGCGCAACCGCCAGGTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAG < SRR3722072.689400/100‑1 (MQ=60)
GTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTAC < SRR3722072.649057/100‑1 (MQ=60)
GTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTAC < SRR3722072.687914/100‑1 (MQ=60)
TCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCAT < SRR3722072.282814/100‑1 (MQ=60)
TCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCAT < SRR3722072.709741/100‑1 (MQ=60)
TCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCAT < SRR3722072.824375/100‑1 (MQ=60)
TCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCAT < SRR3722072.87886/100‑1 (MQ=60)
CACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGAGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGAC < SRR3722072.853922/100‑1 (MQ=60)
|
CAAACGGGATGTTGTTTTCTTCCAGCGCAACCGCCAGGTCCGCCTCAGCACGATCCCACATTTCGTCGCTGCCAATACGTTTTTCAGGACGAGTGGAGAGTTTGACGACGATCTTCTCGAAGCCAAAAGTGCTGTACATATCATAGAC > NZ_CP009273/1795471‑1795618
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
