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 |
2,849,315 |
A→C |
Y540S (TAC→TCC) |
flhA → |
formate hydrogenlyase transcriptional activator FlhA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,849,315 | 0 | A | C | 93.8%
| 44.5
/ ‑6.3
| 16 | Y540S (TAC→TCC) | flhA | formate hydrogenlyase transcriptional activator FlhA |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (7/8); total (7/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTT > NZ_CP009273/2849239‑2849394
|
gTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTa < 1:356416/90‑1 (MQ=255)
cGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTc > 2:320271/1‑90 (MQ=255)
tAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGa > 1:214618/1‑90 (MQ=255)
ccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAcc > 2:267142/1‑90 (MQ=255)
ccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAcc > 2:511598/1‑90 (MQ=255)
aCTACCCGCGATCTGAAAAAAATGGTCCCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccg < 1:549013/90‑1 (MQ=255)
tacccGCGATCTAAAAAAAAGGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccgcc < 2:533378/87‑1 (MQ=255)
aCCGCGATCTGAAAAAAATGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCAc < 1:673919/90‑1 (MQ=255)
ctaaaaaaaaGGGTCCCCGCCCGGGAGTCCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg < 2:105453/87‑1 (MQ=255)
cTGAAAAAAATGGTCGCCGCCCGTGTGTCCCGTAGGGATTTTTTTTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAg < 2:802399/90‑1 (MQ=255)
cTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg < 1:189764/90‑1 (MQ=255)
cTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg < 1:343447/90‑1 (MQ=255)
tGAGTTCCGTAGCGATCTTTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCgctgct < 1:565568/90‑1 (MQ=255)
gTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGc > 2:720975/1‑90 (MQ=255)
cGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaaa > 1:29033/1‑90 (MQ=255)
gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt > 1:653920/1‑90 (MQ=255)
|
GTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTT > NZ_CP009273/2849239‑2849394
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCC > NZ_CP009273/2849217‑2849409
|
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC > SRR3722079.106308/1‑100 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC < SRR3722079.1775/100‑1 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC < SRR3722079.597646/100‑1 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC < SRR3722079.646356/100‑1 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCAGTAGCGATCTCTATTAC < SRR3722079.515635/100‑1 (MQ=60)
GACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGA > SRR3722079.216446/1‑100 (MQ=60)
GTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTC < SRR3722079.359208/100‑1 (MQ=60)
ACTACCCGCGATCTGAAAAAAATGGTCCCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCG < SRR3722079.554266/100‑1 (MQ=60)
ACCGCGATCTGAAAAAAATGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCG < SRR3722079.680981/100‑1 (MQ=60)
CTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAG < SRR3722079.191415/100‑1 (MQ=60)
CTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAG < SRR3722079.346162/100‑1 (MQ=60)
CCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAA > SRR3722079.29248/1‑100 (MQ=60)
TGAGTTCCGTAGCGATCTTTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCC < SRR3722079.571087/100‑1 (MQ=60)
GTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTT > SRR3722079.660688/1‑100 (MQ=60)
CTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCC > SRR3722079.833966/1‑100 (MQ=60)
|
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCC > NZ_CP009273/2849217‑2849409
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
