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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
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 | . | 94.1%
| 60.3
/ ‑1.0
| 17 | coding (52/441 nt) | BW25113_RS06225 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base . (7/9); total (8/9) |
| Fisher's exact test for biased strand distribution p-value = 4.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01 |
ATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAA > NZ_CP009273/1240582‑1240744
|
aTCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATgggcg > 1:714216/1‑88 (MQ=255)
cTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGAt < 2:988441/90‑1 (MQ=255)
cTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGAt < 2:1609/90‑1 (MQ=255)
gttgttTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTg < 1:1182857/90‑1 (MQ=255)
tgttTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTgcg < 1:548185/90‑1 (MQ=255)
ttttGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCt > 2:1459171/1‑84 (MQ=255)
ttttGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCt < 1:1459171/84‑1 (MQ=255)
tGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTAtt < 1:451992/90‑1 (MQ=255)
tgtgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGaa < 2:554648/90‑1 (MQ=255)
tgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGGTTTTGCTGCGCTTATTTaaa > 1:1434637/1‑89 (MQ=255)
aaaaTAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAAt < 1:1451251/90‑1 (MQ=255)
atTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGGTTTTGCTGCGCTTTTTTAAAATTTAGAATTGATTAATc > 1:1177363/1‑90 (MQ=255)
gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTTTTTAAAATTTAGAATTGATTAATCCTTCTGGCAg > 1:366036/1‑90 (MQ=255)
gTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTTGCAGATTAAGc > 2:1457795/1‑90 (MQ=255)
aGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGGTGCGCCTTTTTAAAAATTAGAATTGATTAAACCTTTTGGCAGATTTAGCCaa > 1:1250716/1‑90 (MQ=255)
aGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTTAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCaa > 1:1379425/1‑90 (MQ=255)
aGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGaa < 1:97416/51‑1 (MQ=255)
aGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGaa > 2:97416/1‑51 (MQ=255)
|
ATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAA > NZ_CP009273/1240582‑1240744
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ 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
CGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCG > NZ_CP009273/1240603‑1240756
|
CGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTG < SRR3722078.1482973/100‑1 (MQ=60)
GTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGA < SRR3722078.1201345/100‑1 (MQ=60)
TGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAAC < SRR3722078.554656/100‑1 (MQ=60)
GTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGGTTTTGCTGCGCTTATTtaaa > SRR3722078.1457982/1‑96 (MQ=60)
TGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAG < SRR3722078.457393/100‑1 (MQ=60)
cggcagcgtcagatgtgtataagagacagGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAAT < SRR3722078.98556/71‑1 (MQ=60)
GAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGGTTTTGCTGCGCTTTTTTAAAATTTAGAATTGATTAATC > SRR3722078.1195740/1‑100 (MQ=60)
AAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCC < SRR3722078.1474918/100‑1 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTTTTTAAAATTTAGAATTGATTAATCCTTCTGGCAG > SRR3722078.370506/1‑100 (MQ=60)
ATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGggcctttttaaaaattaaaatttatcaatcctttctgcag > SRR3722078.878471/1‑60 (MQ=60)
GTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGGTGCGCCTTTTTAAAAATTAGAATTGATTAAACCTTTTGGCAGATTTAGCCAA > SRR3722078.1270520/1‑100 (MQ=37)
GTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTTAACATTTAGAATTGATTAAACCTTCTGGCAGATTAAGCCAA > SRR3722078.1401679/1‑100 (MQ=60)
GCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTTTTTAACAATTTGAATTGGTCAATCCTTtttgcgaaataagccaaaaaaaccgtttg > SRR3722078.1540530/1‑71 (MQ=28)
|
CGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCG > NZ_CP009273/1240603‑1240756
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
