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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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 | 100.0%
| 60.5
/ NA
| 20 | Y540S (TAC→TCC) | flhA | formate hydrogenlyase transcriptional activator FlhA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (7/13); total (7/13) |
GACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTT > NZ_CP009273/2849232‑2849394
|
gacggacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCt < 1:73979/90‑1 (MQ=255)
acggacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTg < 1:114180/90‑1 (MQ=255)
acggacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTg < 1:723473/90‑1 (MQ=255)
acgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACg > 2:208142/1‑90 (MQ=255)
gCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTAtt > 1:487723/1‑90 (MQ=255)
cGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGGGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTc < 2:391916/90‑1 (MQ=255)
tCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTccc < 2:376512/90‑1 (MQ=255)
aCTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccg < 2:59944/90‑1 (MQ=255)
tacccGCGATCTAAAAAAAAGGGTCCCCGCCCGGGAGTCCCGTAGCGATCTCTATCCCCGCCTGAACGTATTCCCGATTCCCCTgccgcc < 1:675525/87‑1 (MQ=255)
cccGCGATCTAAAAAAAATGGCCGCCGCCCGTGATTCCCGTAGCGATCTCTTTCCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCAc < 1:429900/89‑1 (MQ=255)
aTCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTAcgcg > 2:463260/1‑90 (MQ=255)
cTGAAAAAATTGGTCGCCGACCGTGAGTTCCGTACCGATCTCTATTCCCGCCCGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg < 1:587044/90‑1 (MQ=255)
tGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGc < 2:269044/90‑1 (MQ=255)
gAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCg > 1:431311/1‑90 (MQ=255)
aaaaTGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCg < 1:201924/90‑1 (MQ=255)
gTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccgcc > 1:391634/1‑58 (MQ=255)
gTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccgcc < 2:391634/58‑1 (MQ=255)
tCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGa > 2:647372/1‑90 (MQ=255)
gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt > 1:164869/1‑90 (MQ=255)
gATCTCTATCCCCGCCTGAACGTTTCCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt < 1:681056/90‑1 (MQ=38)
|
GACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTT > NZ_CP009273/2849232‑2849394
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCCCG > NZ_CP009273/2849216‑2849411
|
GCAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTC < SRR3722112.302162/100‑1 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGGTCTCTATTCC > SRR3722112.344817/1‑100 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC < SRR3722112.160175/100‑1 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC < SRR3722112.677926/100‑1 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC < SRR3722112.259602/100‑1 (MQ=60)
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTCAGTTCCGTAGCGATCTCTATTCC < SRR3722112.697747/100‑1 (MQ=60)
AGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATT > SRR3722112.494752/1‑100 (MQ=60)
GACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTC < SRR3722112.74882/100‑1 (MQ=60)
ACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCC < SRR3722112.734765/100‑1 (MQ=60)
ACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCC < SRR3722112.115601/100‑1 (MQ=60)
TACCCGCGATCTAAAAAAAAGGGTCCCCGCCCGGGAGTCCCGTAGCGATCTCTATCCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAG < SRR3722112.686079/100‑1 (MQ=56)
CCCGCGATCTAAAAAAAATGGCCGCCGCCCGTGATTCCCGTAGCGATCTCTTTCCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCG < SRR3722112.435719/100‑1 (MQ=60)
ACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCG > SRR3722112.437175/1‑100 (MQ=60)
CTGAAAAAATTGGTCGCCGACCGTGAGTTCCGTACCGATCTCTATTCCCGCCCGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAG < SRR3722112.596007/100‑1 (MQ=60)
AAAATGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTC < SRR3722112.204381/100‑1 (MQ=60)
GTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCtgtctcttatacacatctgac > SRR3722112.396759/1‑79 (MQ=60)
GTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagatctcg > SRR3722112.709605/1‑47 (MQ=60)
GTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTT > SRR3722112.166896/1‑100 (MQ=60)
GATCTCTATCCCCGCCTGAACGTTTCCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAA < SRR3722112.691705/100‑1 (MQ=60)
CTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > SRR3722112.29937/1‑100 (MQ=60)
ATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCCCG > SRR3722112.361578/1‑100 (MQ=60)
|
GCAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCCCG > NZ_CP009273/2849216‑2849411
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
