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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 68.3
/ NA
| 17 | coding (52/441 nt) | BW25113_RS06225 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (7/10); total (7/10) |
CAGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGAAC‑ATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACC > NZ_CP009273/1240578‑1240750
|
caGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATg > 1:423353/1‑90 (MQ=255)
gAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATggg > 1:78122/1‑90 (MQ=255)
aTCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATgggcg > 1:129270/1‑88 (MQ=255)
atcattGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGc > 2:716194/4‑90 (MQ=255)
tCGTTGTTTTTGGTGTGATTCAGAAAATAAGTATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGc < 1:689572/90‑1 (MQ=255)
gttTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTgcgc < 1:50551/90‑1 (MQ=255)
tGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑tt < 2:91072/90‑1 (MQ=255)
tGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑tt < 2:129270/90‑1 (MQ=255)
gATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGGTTA‑TTTAAC‑At > 1:620862/1‑90 (MQ=255)
aaataTTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGAAC‑ATTTAGAATTGATc < 2:759319/90‑1 (MQ=255)
aataTTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGACGCGGTTTTGGCTGCGCTTA‑TTGAAC‑ATTTAGAATTGATCa < 2:533491/90‑1 (MQ=255)
tatTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGAAC‑ATTTAGAATTGATCAAt < 2:395072/90‑1 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGGTGCGCCTT‑TTTAAA‑ATTTAGAATTGATCAATCCTTCTGGCAg > 1:59484/1‑90 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGATTGGCTTATTTAAAA‑AATTAAAATTCATCAAACCTTCTGGcg > 1:503616/1‑89 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGGTGCGCTTT‑TTTAAA‑ATTTTGAATTGATCAATCCTTCTGGCAg > 1:453203/1‑90 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGaa > 1:736723/1‑61 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGaa < 2:736723/61‑1 (MQ=255)
gTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGAACAATTTAGAATTCATCAATCCTTCTGGCAGATTAAg < 2:503616/90‑1 (MQ=255)
gCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGAAC‑ATTTAGAATTGATCAAAACTTCTGGCAGATTAAGCCaaaa > 1:363338/1‑90 (MQ=255)
tAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGAAC‑ATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATAcc < 2:668936/90‑1 (MQ=255)
|
CAGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTA‑TTGAAC‑ATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACC > NZ_CP009273/1240578‑1240750
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ 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
ACAACAACAGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATGCTTCAGT > NZ_CP009273/1240571‑1240769
|
ACAACAACAGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGC < SRR3722073.10597/100‑1 (MQ=60)
TCGTTGTTTTTGGTGTGATTCAGAAAATAAGTATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATT < SRR3722073.703618/100‑1 (MQ=60)
GTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACA < SRR3722073.51739/100‑1 (MQ=60)
TTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGGTTATTTAACAT > SRR3722073.633765/1‑100 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTtgattggcttatttaaaaaattaaaattcatcaaaccttctggcg > SRR3722073.514251/1‑55 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGGTGCGCCTTTTTAAAATTTAGAATTGATCAATCCTTCTGGCAG > SRR3722073.60878/1‑100 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTATTTAAAATTTAGAATctgtctcttatacacatct > SRR3722073.751636/1‑81 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGGTGCGCTTTTTTAAAATTTTGAATTGATCAATCCTTCTGGCAG > SRR3722073.462889/1‑100 (MQ=60)
AGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAAAACTTCTGGCAGATTAAGCCAAAA > SRR3722073.371048/1‑100 (MQ=60)
GCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTTGGCAATGCTTCAGT < SRR3722073.730670/100‑1 (MQ=60)
|
ACAACAACAGAATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATGCTTCAGT > NZ_CP009273/1240571‑1240769
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
