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 |
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 | . | 86.7%
| 44.7
/ 4.8
| 15 | coding (52/441 nt) | BW25113_RS06225 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (2/0); new base . (6/7); total (8/7) |
| Fisher's exact test for biased strand distribution p-value = 4.67e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.20e-01 |
AATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTA > NZ_CP009273/1240592‑1240738
|
aaTTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAgg < 2:275762/90‑1 (MQ=255)
tGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGttt < 1:706062/90‑1 (MQ=255)
tgtgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGaa < 2:162738/90‑1 (MQ=255)
tgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTTTTTAACa > 2:219324/1‑90 (MQ=255)
ttCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACAttt < 2:416224/90‑1 (MQ=255)
aaaaTAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAAt < 1:520675/90‑1 (MQ=255)
taaataTTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGAt > 1:101471/1‑90 (MQ=255)
taaataTTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGAt < 2:297917/90‑1 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCa > 1:278012/1‑90 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCa > 1:282152/1‑90 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTATTTAACATTTTGAATTTATCAATCCTTCTGGGAg > 1:834484/1‑90 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTTAAAATTTAGAATTGATCAAACCTTCTGGCAg > 2:353852/1‑90 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTTGCAg > 1:366017/1‑90 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAAAATTTTGAATTTATCAAACCTTCTTGCAg > 2:62644/1‑90 (MQ=255)
ccAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTa < 1:215113/90‑1 (MQ=255)
|
AATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTA > NZ_CP009273/1240592‑1240738
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATA > NZ_CP009273/1240598‑1240748
|
TGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCT < SRR3722079.713552/100‑1 (MQ=60)
ATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGAT > SRR3722079.102283/1‑100 (MQ=60)
AAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCC < SRR3722079.525476/100‑1 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTTGCA > SRR3722079.284494/1‑100 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCA > SRR3722079.280332/1‑100 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTATTTAACATTTTGAATTTATCAATCCTTCTGGGAG > SRR3722079.843417/1‑100 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTTGCAG > SRR3722079.368902/1‑100 (MQ=60)
AGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTtgcctgtctcttatacacatctccgagcccccgagaccagagaggaactcgtatgcc > SRR3722079.705444/1‑43 (MQ=60)
CCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATA < SRR3722079.216947/100‑1 (MQ=60)
|
TGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATA > NZ_CP009273/1240598‑1240748
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
