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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,240,670 |
Δ1 bp |
coding (55/441 nt) |
BW25113_RS06225 → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,240,667 | 0 | G | . | 100.0%
| 60.6
/ NA
| 15 | coding (52/441 nt) | BW25113_RS06225 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (7/8); total (7/8) |
TTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAG > NZ_CP009273/1240589‑1240740
|
tttAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTg > 2:658048/1‑90 (MQ=255)
ttAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGa > 2:329231/1‑90 (MQ=255)
aaTTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAgg < 1:296153/90‑1 (MQ=255)
gttgttTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTg > 1:528616/1‑90 (MQ=255)
gttTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTgcgc > 1:864001/1‑90 (MQ=255)
ttGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTAt < 2:436479/90‑1 (MQ=255)
tgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCGGGGCCTATTTaaaa > 2:662221/1‑88 (MQ=255)
gATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTTTTTAAAAt > 2:85397/1‑90 (MQ=255)
aGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTATTTAACATTTAGa > 2:975652/1‑90 (MQ=255)
aaaaTAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAAt < 1:337570/90‑1 (MQ=255)
aaaaTAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAAt < 2:173287/90‑1 (MQ=255)
cAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGc < 1:1027350/90‑1 (MQ=255)
cAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGc < 1:27403/90‑1 (MQ=255)
cAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGc < 1:658048/90‑1 (MQ=255)
aGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAg < 1:806028/90‑1 (MQ=255)
|
TTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAG > NZ_CP009273/1240589‑1240740
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ 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
ACAGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATGCTTCAGT > NZ_CP009273/1240577‑1240769
|
ACAGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAG < SRR3722089.1048212/100‑1 (MQ=60)
AATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGC < SRR3722089.299934/100‑1 (MQ=60)
TTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTG > SRR3722089.534785/1‑100 (MQ=60)
TTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGC > SRR3722089.876369/1‑100 (MQ=60)
AAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCC < SRR3722089.341779/100‑1 (MQ=60)
CAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCC < SRR3722089.1042680/100‑1 (MQ=60)
CAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCC < SRR3722089.27734/100‑1 (MQ=60)
CAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCC < SRR3722089.666528/100‑1 (MQ=60)
AGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACC < SRR3722089.817243/100‑1 (MQ=60)
GGCGGATAGTGAGGCGGTTTTTGGTGCGCTTTTTGAACATTTTGAATTGATCAATCCTTCTGGCGGATTAAGCCAAAAAACCCGTTCGGCAATGCTTCAG > SRR3722089.784105/1‑100 (MQ=60)
GCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATGCTTCAGT < SRR3722089.751472/100‑1 (MQ=60)
|
ACAGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATGCTTCAGT > NZ_CP009273/1240577‑1240769
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
