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 F1 I1 R1
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260480 |
2,737,505 |
Δ1 bp |
intergenic (‑222/+22) |
h16_B2423 ← / ← h16_B2424 |
periplasmic solute binding protein/Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 2,737,504 | 0 | A | . | 100.0%
| 82.5
/ NA
| 19 | intergenic (‑221/+23) | h16_B2423/h16_B2424 | periplasmic solute binding protein/Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (10/9); total (10/9) |
TAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCG > AM260480/2737384‑2737621
|
tAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACg < 2:204151/133‑1 (MQ=255)
cTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGtt < 2:364351/134‑1 (MQ=255)
aTGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAgg > 2:787712/1‑133 (MQ=255)
cggcAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGgcgc > 1:924591/1‑134 (MQ=255)
ccagccagCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATggcgg > 2:38585/1‑134 (MQ=255)
ccagccagCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATggcgg > 1:913547/1‑134 (MQ=255)
cagccagcGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATggcggg > 1:325119/1‑134 (MQ=255)
aCGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTgg > 1:367264/1‑134 (MQ=255)
cgcgcgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACg > 1:516209/1‑59 (MQ=255)
cgcgcgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACg < 2:516209/59‑1 (MQ=255)
cgcgcgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTggc < 1:38585/134‑1 (MQ=255)
cgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTc > 1:631380/1‑66 (MQ=255)
cgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTc < 2:631380/66‑1 (MQ=255)
ttGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGc < 2:763835/133‑1 (MQ=255)
aaTCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCaa < 1:733202/92‑1 (MQ=255)
aaTCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCaa > 2:733202/1‑92 (MQ=255)
ggACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCcg < 2:913547/134‑1 (MQ=255)
gggAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAAt > 1:803931/1‑83 (MQ=255)
gggAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAAt < 2:803931/83‑1 (MQ=255)
|
TAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCG > AM260480/2737384‑2737621
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
BRESEQ :: bam2aln output
GGGCCGGTGCCGGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGTGCGGTGTCCGCA > AM260480/2737367‑2737653
|
ttctttctttcctgcgtttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAAC < GWNJ‑0478:712:GW2002102894th:2:1115:18220:16578/57‑1 (MQ=57)
GCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTctgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:2107:5192:73259/1‑136 (MQ=60)
CGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCG > GWNJ‑0478:712:GW2002102894th:2:2211:9948:82954/1‑150 (MQ=60)
gtcgctgactcccgtccctgattcccgccgcgcggcaacaCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGG > GWNJ‑0478:712:GW2002102894th:2:2202:2625:71723/41‑150 (MQ=60)
CCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGG > GWNJ‑0478:712:GW2002102894th:2:2211:6331:18281/1‑150 (MQ=60)
CGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGC > GWNJ‑0478:712:GW2002102894th:2:1204:20588:79362/1‑150 (MQ=60)
gggctcggagatgtgtataagagacaGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGG < GWNJ‑0478:712:GW2002102894th:2:2115:14374:72256/123‑1 (MQ=60)
cccgtccctgattcccgcCGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGG < GWNJ‑0478:712:GW2002102894th:2:2115:12958:71113/130‑1 (MQ=60)
GCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGC > GWNJ‑0478:712:GW2002102894th:2:1208:17529:47000/1‑150 (MQ=60)
ccctgattccCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttct > GWNJ‑0478:712:GW2002102894th:2:1216:4313:84491/11‑89 (MQ=60)
AGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgcc > GWNJ‑0478:712:GW2002102894th:2:2108:9310:71369/1‑97 (MQ=60)
ACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGC < GWNJ‑0478:712:GW2002102894th:2:1105:19961:66827/150‑1 (MQ=60)
GCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTctgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:2202:11717:14557/1‑113 (MQ=60)
TCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGG > GWNJ‑0478:712:GW2002102894th:2:1202:3549:5888/1‑150 (MQ=60)
GGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGC > GWNJ‑0478:712:GW2002102894th:2:1209:2393:18211/1‑67 (MQ=60)
gcgacATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgctt > GWNJ‑0478:712:GW2002102894th:2:2207:10866:80959/6‑85 (MQ=60)
CATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGTGCGGTGTCCGCA < GWNJ‑0478:712:GW2002102894th:2:2206:15762:87696/150‑1 (MQ=60)
|
GGGCCGGTGCCGGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGTGCGGTGTCCGCA > AM260480/2737367‑2737653
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
