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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 38.0
/ NA
| 13 | Y540S (TAC→TCC) | flhA | formate hydrogenlyase transcriptional activator FlhA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (6/7); total (6/7) |
GACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAA > NZ_CP009273/2849232‑2849387
|
gacggacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCt > 1:156539/1‑90 (MQ=255)
gacggacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCt < 2:452816/90‑1 (MQ=255)
acgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACg > 2:315177/1‑90 (MQ=255)
gCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTAtt > 1:194057/1‑90 (MQ=255)
tAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGa > 1:122796/1‑90 (MQ=255)
ccaCTACCCGCGATCTGAAAAAAAGGGTCCCCGCCCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgc < 2:354924/88‑1 (MQ=255)
aCTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccg < 2:235226/90‑1 (MQ=255)
aaaaTGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCg < 2:156539/90‑1 (MQ=255)
gTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGat > 1:525557/1‑90 (MQ=255)
gTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGat < 2:259578/90‑1 (MQ=255)
ccGTAGGGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa < 2:525557/90‑1 (MQ=38)
gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCgctgc > 1:249096/1‑76 (MQ=255)
gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCgctgc < 2:249096/76‑1 (MQ=255)
|
GACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAA > NZ_CP009273/2849232‑2849387
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > NZ_CP009273/2849217‑2849407
|
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC < SRR3722092.501795/100‑1 (MQ=60)
AAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCT > SRR3722092.159164/1‑100 (MQ=60)
AGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATT > SRR3722092.197280/1‑100 (MQ=60)
GACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGA > SRR3722092.124876/1‑100 (MQ=60)
ccaccgagatctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCAC < SRR3722092.324731/43‑1 (MQ=60)
GAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGAT > SRR3722092.536097/1‑100 (MQ=60)
GTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTGT > SRR3722092.253128/1‑100 (MQ=60)
CTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > SRR3722092.178977/1‑100 (MQ=60)
CTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > SRR3722092.433621/1‑100 (MQ=60)
CTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > SRR3722092.467106/1‑100 (MQ=60)
|
CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > NZ_CP009273/2849217‑2849407
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
