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 |
|
A12 F1 I1 R1
|
760 |
58.2 |
3022526 |
90.8% |
2744453 |
102.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,673,345 |
(T)7→8 |
coding (157/366 nt) |
mdtJ ← |
multidrug efflux system transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,673,338 | 1 | . | T | 96.7%
| 188.3
/ ‑0.9
| 60 | coding (164/366 nt) | mdtJ | multidrug efflux system transporter |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base T (30/28); total (31/29) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01 |
GGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑TTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCC > NC_000913/1673219‑1673472
|
gggTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAag > 1:1220192/1‑139 (MQ=255)
tggtTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑tttttttt > 1:766115/1‑124 (MQ=255)
tggtTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑tttttttt < 2:766115/125‑2 (MQ=255)
ggtTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAagagag < 2:1220192/139‑1 (MQ=255)
ttAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGa > 1:453104/1‑130 (MQ=255)
ttAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGa < 2:453104/130‑1 (MQ=255)
cGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGaa > 2:833164/1‑133 (MQ=255)
cGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGaa < 1:833164/133‑1 (MQ=255)
ggCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGaaa > 2:373912/1‑125 (MQ=255)
ggCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGaaa < 1:373912/125‑1 (MQ=255)
aaaCTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc < 2:230778/139‑1 (MQ=255)
tcgAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAag < 2:449629/98‑1 (MQ=255)
tcgAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAag > 1:449629/1‑98 (MQ=255)
aaCGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgccgcc < 1:1477414/139‑1 (MQ=255)
cGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCAt > 1:494453/1‑122 (MQ=255)
cGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCAt < 2:494453/122‑1 (MQ=255)
ggTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc < 1:1284792/107‑1 (MQ=255)
ggTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc > 2:1284792/1‑107 (MQ=255)
taaataaaATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑TTTTTTTAAACGGCGAAAGAGAGAAatata > 2:453393/1‑81 (MQ=255)
taaataaaATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑TTTTTTTAAACGGCGAAAGAGAGAAatata < 1:453393/81‑1 (MQ=255)
aataCCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAc > 2:1283223/1‑94 (MQ=255)
aataCCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAc < 1:1283223/94‑1 (MQ=255)
taCCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCAtt > 2:1407015/1‑139 (MQ=255)
aTACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCAt > 2:1511046/1‑133 (MQ=255)
aTACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCAt < 1:1511046/133‑1 (MQ=255)
aTACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCAtt > 1:1133261/1‑139 (MQ=255)
aTACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCAtt > 1:1242587/1‑139 (MQ=255)
tCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGaa < 2:667259/56‑1 (MQ=39)
tCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGaa > 1:667259/1‑56 (MQ=39)
cccACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACt < 1:281183/113‑1 (MQ=255)
cccACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACt > 2:281183/1‑113 (MQ=255)
cccACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCg > 2:1097806/1‑139 (MQ=255)
aGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGa > 2:1128692/1‑129 (MQ=255)
aGCGCATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGa < 1:1128692/129‑1 (MQ=255)
gcgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc < 1:131912/75‑1 (MQ=255)
gcgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc > 2:131912/1‑75 (MQ=255)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAagaga > 2:736566/1‑45 (MQ=38)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAagaga < 1:736566/45‑1 (MQ=38)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGaa > 2:577190/1‑48 (MQ=38)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGaa < 1:577190/48‑1 (MQ=38)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgc < 2:54197/90‑1 (MQ=255)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgc > 1:54197/1‑90 (MQ=255)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCAt > 1:177105/1‑119 (MQ=255)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCAt < 2:177105/119‑1 (MQ=255)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGt > 1:775441/1‑139 (MQ=255)
cgcATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAG‑AATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTa > 2:830841/1‑139 (MQ=255)
cATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAatata > 1:650573/1‑51 (MQ=38)
cATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAatata < 2:650573/51‑1 (MQ=38)
cATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGaaa < 2:427959/64‑1 (MQ=255)
cATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGaaa > 1:427959/1‑64 (MQ=255)
cATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAatc < 2:250218/66‑1 (MQ=255)
cATAAGCTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAatc > 1:250218/1‑66 (MQ=255)
cTACGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTg < 2:1133261/139‑1 (MQ=255)
aCGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTa > 2:382757/1‑139 (MQ=255)
cGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAg < 1:574825/78‑1 (MQ=255)
cGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAg > 2:574825/1‑78 (MQ=255)
cGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTg > 2:1013182/1‑136 (MQ=255)
cGCCTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTg < 1:1013182/136‑1 (MQ=255)
ccTAAGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCa < 1:1097806/139‑1 (MQ=255)
aGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCAt > 2:179595/1‑102 (MQ=255)
aGGCGATTTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCAt < 1:179595/102‑1 (MQ=255)
ggCGATTTTTTTT‑AACGGCGAAAGAGAG‑AATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGcc < 1:830841/139‑1 (MQ=255)
|
GGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑TTTTTTT‑AACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCC > NC_000913/1673219‑1673472
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
