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 |
901,740 |
G→A |
A157V (GCG→GTG) |
ybjS ← |
NAD(P)‑dependent oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 901,740 | 0 | G | A | 96.4%
| 94.6
/ ‑3.9
| 28 | A157V (GCG→GTG) | ybjS | NAD(P)‑dependent oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (17/10); total (18/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01 |
ATATGCGCCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCGCCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGAAAATCT > NZ_CP009273/901653‑901823
|
atatGCGCCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCAcc > 1:761958/1‑90 (MQ=255)
tGCGCCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGc > 2:774453/1‑90 (MQ=255)
gcgcCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCg < 2:134650/90‑1 (MQ=255)
cgcCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGa > 1:111342/1‑90 (MQ=255)
gcCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGaa > 2:287145/1‑90 (MQ=255)
gcCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGaa < 2:111342/90‑1 (MQ=255)
gACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCGCCTGCGAAAGCa > 2:662093/1‑90 (MQ=255)
aTAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATc < 2:811501/90‑1 (MQ=255)
tAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCa > 1:184711/1‑90 (MQ=255)
tttATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACttcttc > 2:229229/1‑90 (MQ=255)
tATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCgc > 1:751450/1‑90 (MQ=255)
tATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCgc > 2:21052/1‑90 (MQ=255)
gTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCgctggc < 2:135124/90‑1 (MQ=255)
gTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCtt > 2:810274/1‑90 (MQ=255)
gACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCggg > 2:335427/1‑90 (MQ=255)
aCTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGc > 1:328275/1‑90 (MQ=255)
tttGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCaa > 1:110753/1‑90 (MQ=255)
tAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGc < 2:110753/90‑1 (MQ=255)
aaGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGa < 2:551722/90‑1 (MQ=255)
aaGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGa < 2:646314/90‑1 (MQ=255)
aGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAg < 2:296286/90‑1 (MQ=255)
gcgcGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAgg > 2:375046/1‑90 (MQ=255)
gcgcGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAgg > 2:533460/1‑90 (MQ=255)
gcgcGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAgg > 1:192607/1‑90 (MQ=255)
gcgcGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAgg > 2:682879/1‑90 (MQ=255)
gcgTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGc < 1:794226/90‑1 (MQ=255)
gTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGa > 2:206571/1‑90 (MQ=255)
ggATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGAAAAtct < 1:639316/90‑1 (MQ=255)
|
ATATGCGCCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCGCCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGAAAATCT > NZ_CP009273/901653‑901823
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
GTGGTGCATCATATGCGCCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCGCCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGAAAATCTTCTTTAATAT > NZ_CP009273/901643‑901833
|
GTGGTGCATCATATGCGCCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACC > SRR3722072.775388/1‑100 (MQ=60)
GCATCATATGCGCCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGA > SRR3722072.113400/1‑100 (MQ=60)
AGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCA > SRR3722072.187912/1‑100 (MQ=60)
ATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGC > SRR3722072.764727/1‑100 (MQ=60)
GTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGC > SRR3722072.334042/1‑100 (MQ=60)
CCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAA > SRR3722072.112798/1‑100 (MQ=60)
GAATAGTAAAGCGCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGG > SRR3722072.195941/1‑100 (MQ=60)
GCGTTTGTGGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGAAAATCTTC < SRR3722072.808122/100‑1 (MQ=60)
GGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGAAAATCTTCTTTAATAT < SRR3722072.650726/100‑1 (MQ=60)
GGATTCACCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGAAAATCTTCTTTAATAT > SRR3722072.841970/1‑100 (MQ=60)
|
GTGGTGCATCATATGCGCCAGACGGGGAATAAAGACTTTATCGTGCGGTCCGAACAGACTTTGTGGGCGCAGAATAGTAAAGCGCGTTTGTGGATTCGCCTGCGAAAGCATATTGATCACTTCTTCGCTGGCTGCTTTGCTGCGGGCAAACTCGTTGGCGAAGCGGTGAGGGCGAAAATCTTCTTTAATAT > NZ_CP009273/901643‑901833
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
