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 |
3,798,416 |
(T)8→7 |
coding (61/936 nt) |
rfaS ← |
LPS core biosynthesis protein RfaS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,798,409 | 0 | T | . | 90.0%
| 24.5
/ 0.6
| 11 | coding (68/936 nt) | rfaS | LPS core biosynthesis protein RfaS |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (5/4); total (5/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01 |
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCC > NZ_CP009273/3798328‑3798491
|
gCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACtttttttca < 1:114727/90‑3 (MQ=255)
gCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACtttttttca > 2:736399/1‑88 (MQ=255)
ttATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGt > 2:163774/1‑90 (MQ=255)
atccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTAc > 2:414312/1‑90 (MQ=255)
tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt > 1:637665/1‑90 (MQ=255)
atatTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAAtttctg < 1:37059/90‑4 (MQ=255)
atTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTataaa > 2:206643/1‑90 (MQ=255)
tGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAaataaata < 1:157894/90‑1 (MQ=255)
tgttgtTATATTTTTTATCTTGT‑CCTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTc < 1:248931/90‑1 (MQ=255)
gttgttATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTc < 2:345948/90‑1 (MQ=255)
ttttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagtta < 1:680654/90‑1 (MQ=255)
ttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagttagt > 2:43722/1‑90 (MQ=255)
tCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTcc < 2:637665/90‑1 (MQ=255)
|
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCC > NZ_CP009273/3798328‑3798491
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ 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
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTAATAAATATTTTT > NZ_CP009273/3798328‑3798514
|
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAT < SRR3722073.117191/100‑1 (MQ=60)
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAT > SRR3722073.650826/1‑100 (MQ=60)
ATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTctgtctcttatac < SRR3722073.37975/100‑14 (MQ=60)
TGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAA < SRR3722073.161086/100‑1 (MQ=60)
TGTTGTTATATTTTTTATCTTGT‑CCTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGT < SRR3722073.254157/100‑1 (MQ=60)
TTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTAC < SRR3722073.694554/100‑1 (MQ=60)
CTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTAATAAAT < SRR3722073.142591/100‑1 (MQ=60)
CTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTAATAAAT < SRR3722073.743185/100‑1 (MQ=60)
TTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTAATAAATATTTTT > SRR3722073.29296/1‑100 (MQ=60)
|
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTAATAAATATTTTT > NZ_CP009273/3798328‑3798514
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
