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 |
2,414,135 |
T→C |
G12G (GGT→GGC) |
yfcG → |
GSH‑dependent disulfide bond oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,414,135 | 0 | T | C | 97.2%
| 121.6
/ ‑3.8
| 36 | G12G (GGT→GGC) | yfcG | GSH‑dependent disulfide bond oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (19/16); total (19/17) |
| Fisher's exact test for biased strand distribution p-value = 4.72e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.97e-01 |
CCGCGCTTTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGTCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGGCGGTCA > NZ_CP009273/2414049‑2414212
|
ccgcGCTTTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGTTCTCTATTTCGCCCCGACACCCAATGGCcac < 1:528693/90‑1 (MQ=255)
ttGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCcac < 2:22850/75‑1 (MQ=255)
ttGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCcac > 1:22850/1‑75 (MQ=255)
ttGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGttt > 2:851395/1‑90 (MQ=255)
ttGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGttt > 1:343794/1‑90 (MQ=255)
tgtgGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTtc > 2:593501/1‑90 (MQ=255)
gtggtgTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTtct > 1:902589/1‑90 (MQ=255)
gtggtgTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTtct > 1:459040/1‑90 (MQ=255)
gtggtgTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTtct > 1:430927/1‑90 (MQ=255)
tgtTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCgaa > 1:145013/1‑90 (MQ=255)
gtTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCgaag > 1:690710/1‑90 (MQ=255)
aGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGc < 1:306181/90‑1 (MQ=255)
ttAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCt > 2:621832/1‑90 (MQ=255)
ttAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCt > 1:228139/1‑90 (MQ=255)
tAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTg < 2:690710/90‑1 (MQ=255)
acCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTAt > 2:65520/1‑90 (MQ=255)
ggAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGc < 1:650327/90‑1 (MQ=255)
ggAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGc < 1:770571/90‑1 (MQ=255)
gAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGTCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCt < 1:348783/90‑1 (MQ=255)
gAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCt < 1:180661/90‑1 (MQ=255)
gCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGc > 1:705899/1‑55 (MQ=255)
gCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGc < 2:705899/55‑1 (MQ=255)
gCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGAtt < 2:530505/90‑1 (MQ=255)
aaTGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTaa < 1:477942/90‑1 (MQ=255)
tGATCGATCTCTATTTCGCCCCGACACCCAATGGCCAC‑AAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGt < 1:581486/90‑1 (MQ=255)
gatcgatcTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGt < 2:607401/90‑1 (MQ=255)
atcgatcTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTa < 2:145013/90‑1 (MQ=255)
cGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAgg < 2:430927/90‑1 (MQ=255)
cGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAgg > 1:554538/1‑90 (MQ=255)
gCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGAtt > 1:700612/1‑69 (MQ=255)
gCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGAtt < 2:700612/69‑1 (MQ=255)
gCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGGc > 2:659911/1‑90 (MQ=255)
ccGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGAtt > 2:273091/1‑66 (MQ=255)
ccGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGAtt < 1:273091/66‑1 (MQ=255)
gACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGGCGGTCa > 2:13662/1‑90 (MQ=255)
gACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGGCGGTCa > 1:324187/1‑90 (MQ=255)
|
CCGCGCTTTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGTCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGGCGGTCA > NZ_CP009273/2414049‑2414212
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
CCGCGCTTTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGTCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGGCGGTCA > NZ_CP009273/2414049‑2414212
|
CCGCGCTTTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGTTCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGC < SRR3722072.538212/100‑1 (MQ=60)
CTTTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCctgtc > SRR3722072.23253/1‑95 (MQ=60)
CTTTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTT > SRR3722072.349856/1‑100 (MQ=60)
TTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCT > SRR3722072.467454/1‑100 (MQ=60)
TTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCT > SRR3722072.918126/1‑100 (MQ=60)
TTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCT > SRR3722072.438773/1‑100 (MQ=60)
ATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAA > SRR3722072.147595/1‑100 (MQ=60)
TACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAG > SRR3722072.703064/1‑100 (MQ=60)
GTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCT > SRR3722072.231971/1‑100 (MQ=60)
AGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGAT < SRR3722072.311485/100‑1 (MQ=60)
AACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGActgtctcttatacacatctccgagc > SRR3722072.718493/1‑75 (MQ=60)
GGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGG < SRR3722072.661937/100‑1 (MQ=60)
GGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGG < SRR3722072.784118/100‑1 (MQ=60)
GAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGTCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGT < SRR3722072.354931/100‑1 (MQ=60)
GAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGT < SRR3722072.183786/100‑1 (MQ=60)
tgtataagagacagCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACC < SRR3722072.277758/86‑1 (MQ=60)
AATGATCGATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTG < SRR3722072.486632/100‑1 (MQ=60)
TGATCGATCTCTATTTCGCCCCGACACCCAATGGCCAC‑AAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGG < SRR3722072.591869/100‑1 (MQ=60)
ATCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGG > SRR3722072.564499/1‑100 (MQ=60)
TCTCTATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCctgtctcttat > SRR3722072.713125/1‑89 (MQ=60)
ATTTCGCCCCGACACCCAATGGCCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGGCGGTCA > SRR3722072.329863/1‑100 (MQ=60)
|
CCGCGCTTTCTATACTTGTGGTGTTCAGATGATTAAACAACCGGAGCTGCAATGATCGATCTCTATTTCGCCCCGACACCCAATGGTCACAAAATTACGCTGTTTCTCGAAGAAGCAGAGCTGGATTATCGCTTGATTAAGGTAGACCTGGGGAAAGGCGGTCA > NZ_CP009273/2414049‑2414212
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
