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
|
66 |
46.7 |
5280542 |
98.1% |
5180211 |
47.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,115,117 |
C→T |
pseudogene (358/2509 nt) |
vgrG → |
type VI secretion system tip protein VgrG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,115,117 | 0 | C | T | 100.0%
| 29.2
/ NA
| 10 | pseudogene (358/2509 nt) | vgrG | type VI secretion system tip protein VgrG |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (6/4); total (6/4) |
GAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATCTACCAGAATCTGACGGTG > NC_017635/3115073‑3115135
|
gAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTa < 1:700317/47‑1 (MQ=255)
gAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTa < 2:2086187/47‑1 (MQ=255)
gAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTa < 2:2189067/47‑1 (MQ=255)
aTGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGaac > 1:742199/1‑44 (MQ=255)
aTGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGaac > 2:1493747/1‑44 (MQ=255)
aTGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGaac > 2:2098952/1‑44 (MQ=255)
aTGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGaac > 2:940585/1‑44 (MQ=255)
aTGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGaaa > 1:1969188/1‑44 (MQ=255)
ggCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGAACCAGAc > 1:1819587/1‑48 (MQ=11)
ctgctgACCCGCAGCCGCCAGAATGCCATTTACCAGAACCAGACtgtg < 1:1857696/48‑1 (MQ=11)
|
GAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATCTACCAGAATCTGACGGTG > NC_017635/3115073‑3115135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGGCTTGAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > NC_017635/3115067‑3115163
|
CGGCTTGAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATT < M01420:84:000000000‑ABVEH:1:2104:14684:9808/51‑1 (MQ=60)
GGCTTGAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTT < M01420:84:000000000‑ABVEH:1:2112:11657:12292/51‑1 (MQ=60)
GGCTTGAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTT < M01420:84:000000000‑ABVEH:1:1107:5046:15872/51‑1 (MQ=60)
TGAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACC < M01420:84:000000000‑ABVEH:1:2113:2233:16322/50‑1 (MQ=60)
TGAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACC < M01420:84:000000000‑ABVEH:1:1107:10213:2564/50‑1 (MQ=60)
GTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGAACC > M01420:84:000000000‑ABVEH:1:1107:8550:12466/1‑48 (MQ=24)
GTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGAAAC > M01420:84:000000000‑ABVEH:1:2103:28077:21744/1‑48 (MQ=24)
ATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGAAccagact > M01420:84:000000000‑ABVEH:1:2102:2417:14934/1‑44 (MQ=24)
ATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGAACCAGAC < M01420:84:000000000‑ABVEH:1:2113:19388:6082/50‑1 (MQ=12)
GCTGCTGACCCGCAGCCGCCAGAATGCCATTTACCAGAAccagactgtgtc < M01420:84:000000000‑ABVEH:1:2102:22798:22512/51‑13 (MQ=24)
CCGCCAGAATGCCATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAA < M01420:84:000000000‑ABVEH:1:2106:15447:2120/51‑1 (MQ=0)
GAATGCCATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAAAATCCT > M01420:84:000000000‑ABVEH:1:1111:19407:27331/1‑51 (MQ=0)
AATGCCATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAAAATCCTG > M01420:84:000000000‑ABVEH:1:1101:2127:15723/1‑51 (MQ=0)
AATGCCATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTG > M01420:84:000000000‑ABVEH:1:1114:13668:28792/1‑51 (MQ=0)
GCCATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAAAATCCTGCGC > M01420:84:000000000‑ABVEH:1:1102:16293:14342/1‑51 (MQ=0)
GCCATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGC > M01420:84:000000000‑ABVEH:1:1107:18563:26369/1‑51 (MQ=0)
GCCATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGC > M01420:84:000000000‑ABVEH:1:1102:20564:4407/1‑51 (MQ=0)
ATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:1113:14187:19456/1‑49 (MQ=0)
ATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:1105:9798:19977/1‑49 (MQ=0)
ATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:2109:12944:7139/1‑49 (MQ=0)
ATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:2109:8701:10770/1‑49 (MQ=0)
ATTTACCAGAACCAGACTGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:1103:21073:12472/1‑49 (MQ=0)
ATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:1113:19536:25254/1‑49 (MQ=0)
ATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:2102:14952:25909/1‑49 (MQ=0)
ATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:2102:15181:15984/1‑49 (MQ=0)
ATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:1110:10869:8073/1‑49 (MQ=0)
ATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:1109:8702:11741/1‑49 (MQ=0)
ATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > M01420:84:000000000‑ABVEH:1:2112:13144:8412/1‑49 (MQ=0)
|
CGGCTTGAACCCCGTATGGCGCTGCTGACCCGCAGCCGCCAGAATGCCATCTACCAGAATCTGACGGTGCCGCAAATCGTCGAAAAAATCCTGCGCG > NC_017635/3115067‑3115163
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
