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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,751,237 |
A→G |
V241V (GTT→GTC) |
BW25113_RS13685 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,751,237 | 0 | A | G | 83.9%
| 63.1
/ 9.4
| 31 | V241V (GTT→GTC) | BW25113_RS13685 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (2/3); new base G (11/15); total (13/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.44e-01 |
CAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTC > NZ_CP009273/2751152‑2751312
|
cAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACag < 2:118134/90‑1 (MQ=255)
aTTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCattaatt < 1:176057/90‑1 (MQ=255)
cccATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACt < 2:544218/90‑1 (MQ=255)
cacaGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTc < 2:550183/87‑1 (MQ=255)
ggTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGa < 1:158454/90‑1 (MQ=255)
ggTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGa > 1:653852/1‑90 (MQ=255)
ggTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGa > 2:731882/1‑90 (MQ=255)
gTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGaa > 1:244772/1‑90 (MQ=255)
ttCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAAt < 1:225928/90‑1 (MQ=255)
ttCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAAt < 2:584879/90‑1 (MQ=255)
gATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGt > 1:196337/1‑82 (MQ=255)
gATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGt < 2:316420/82‑1 (MQ=255)
gATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGt > 1:316420/1‑82 (MQ=255)
gATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGt < 2:196337/82‑1 (MQ=255)
tAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGatat < 1:657979/90‑1 (MQ=255)
ttCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTa > 2:36083/1‑90 (MQ=255)
ttAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACt > 1:206737/1‑90 (MQ=255)
tGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAAt > 2:123501/1‑72 (MQ=255)
tGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAAt < 1:123501/72‑1 (MQ=255)
tGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCgc > 1:631264/1‑90 (MQ=255)
tACAACCTTATTTTTCCACCCATCATTCGGGACag < 2:139684/35‑1 (MQ=39)
tACAACCTTATTTTTCCACCCATCATTCGGGACag > 1:139684/1‑35 (MQ=39)
aTTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGcc < 2:73808/90‑1 (MQ=255)
aTTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGcc < 2:211232/90‑1 (MQ=255)
tCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCct > 1:103146/1‑90 (MQ=255)
ccACCCATCATTCGGGACAGAGTCATT‑ATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCcttc < 2:811358/90‑1 (MQ=255)
cACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCcttc < 2:148606/90‑1 (MQ=255)
cACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCcttc < 1:766673/90‑1 (MQ=255)
cACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCcttc > 1:432543/1‑90 (MQ=255)
ttCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAAt > 1:738498/1‑44 (MQ=255)
ttCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAAt < 2:738498/44‑1 (MQ=255)
|
CAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTC > NZ_CP009273/2751152‑2751312
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTCCGCCTGACTTC > NZ_CP009273/2751140‑2751335
|
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGAC < SRR3722079.597464/100‑1 (MQ=60)
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGAC < SRR3722079.345657/100‑1 (MQ=60)
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGAC < SRR3722079.203430/100‑1 (MQ=60)
ATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCA < SRR3722079.177591/100‑1 (MQ=60)
ATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGA > SRR3722079.660620/1‑100 (MQ=60)
TCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAA > SRR3722079.246835/1‑100 (MQ=60)
ATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGAT > SRR3722079.198028/1‑100 (MQ=60)
ATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGAT > SRR3722079.318972/1‑100 (MQ=60)
GGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGT < SRR3722079.159829/100‑1 (MQ=60)
agagacagGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTAC < SRR3722079.124515/92‑1 (MQ=60)
TTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTAC < SRR3722079.227850/100‑1 (MQ=60)
GATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACT > SRR3722079.208514/1‑100 (MQ=60)
TAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTC < SRR3722079.664806/100‑1 (MQ=60)
GTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGC > SRR3722079.637717/1‑100 (MQ=60)
CATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATctgtctcttatacacatctccgagcccacgagaccagagaggatc > SRR3722079.140871/1‑55 (MQ=60)
ACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCT > SRR3722079.103971/1‑100 (MQ=60)
CTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTC > SRR3722079.436289/1‑100 (MQ=60)
CCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACctgtctcttatacacatctccgagcccacgagacca > SRR3722079.746390/1‑64 (MQ=60)
CACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCAC < SRR3722079.774876/100‑1 (MQ=60)
CCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTC > SRR3722079.165436/1‑100 (MQ=60)
GGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTCCGCCTGACTTC > SRR3722079.806839/1‑100 (MQ=60)
|
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTCCGCCTGACTTC > NZ_CP009273/2751140‑2751335
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
