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 |
3,127,257 |
G→A |
pseudogene (573/1425 nt) |
tssA → |
type VI secretion system protein TssA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,127,257 | 0 | G | A | 100.0%
| 56.0
/ NA
| 15 | pseudogene (573/1425 nt) | tssA | type VI secretion system protein TssA |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (1/14); total (1/14) |
GGCTGGCTTTCGGCGCACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAA > NC_017635/3127243‑3127299
|
ggctggctTTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGaca > 1:1979778/1‑46 (MQ=255)
gctTTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGc < 1:1520945/47‑1 (MQ=255)
gctTTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGc < 2:1499616/47‑1 (MQ=255)
gctTTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGc < 2:1552713/47‑1 (MQ=255)
gctTTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGc < 2:784672/47‑1 (MQ=255)
tCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGa < 1:1112468/47‑1 (MQ=255)
tCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGa < 1:96062/47‑1 (MQ=255)
tCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGa < 2:1416835/47‑1 (MQ=255)
tCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGa < 2:2081047/47‑1 (MQ=255)
tCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGa < 2:2099891/47‑1 (MQ=255)
tCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGa < 2:2584373/47‑1 (MQ=255)
tCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGa < 2:598839/47‑1 (MQ=255)
cGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGaa < 1:2625963/47‑1 (MQ=255)
cGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGaa < 1:867341/47‑1 (MQ=255)
cGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGaa < 2:212609/47‑1 (MQ=255)
|
GGCTGGCTTTCGGCGCACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAA > NC_017635/3127243‑3127299
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGTGCTGGCCCGTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCGCACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAACT > NC_017635/3127209‑3127301
|
AGTGCTGGCCCGTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCAC > M01420:84:000000000‑ABVEH:1:1114:20634:19452/1‑50 (MQ=0)
GCTGGCCCGTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCACACCG > M01420:84:000000000‑ABVEH:1:1114:13657:2163/1‑51 (MQ=0)
GCTGGCCCGTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCACACC < M01420:84:000000000‑ABVEH:1:2108:27950:16459/50‑1 (MQ=0)
GCTGGCCCGTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCACACC < M01420:84:000000000‑ABVEH:1:2106:3027:20185/50‑1 (MQ=0)
GCCCGTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCGCACCGGCTG > M01420:84:000000000‑ABVEH:1:2105:18531:24416/1‑51 (MQ=0)
CGTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCGCTCCGGCTGATG < M01420:84:000000000‑ABVEH:1:2114:3503:13173/51‑1 (MQ=0)
GTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCGCACCGGCTGATG > M01420:84:000000000‑ABVEH:1:1105:13012:7258/1‑50 (MQ=0)
GTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCGCACCGGCTGATG > M01420:84:000000000‑ABVEH:1:2109:22414:21946/1‑50 (MQ=0)
GTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCACACCGGCTGATG > M01420:84:000000000‑ABVEH:1:1112:18346:8215/1‑50 (MQ=0)
GTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCACACCGGCTGATG > M01420:84:000000000‑ABVEH:1:1114:2631:17244/1‑50 (MQ=0)
CTGAACGAACAGCCGCAGGGCTGGCTTTCGGCGCACCGGCTGATGAAAACC > M01420:84:000000000‑ABVEH:1:2106:9485:9322/1‑51 (MQ=0)
GAACGAACAGCCGCAGGGCTGGCTTTCGGCACACCGGCTGATGAAAACAC < M01420:84:000000000‑ABVEH:1:2112:4546:11720/50‑1 (MQ=0)
ACGAACAGCCGCAGGGCTGGCTTTCGGCGCACCGGCTGATGAAAACCCTGC < M01420:84:000000000‑ABVEH:1:2106:23658:18432/51‑1 (MQ=0)
AGGGCTGGCTTTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACAC > M01420:84:000000000‑ABVEH:1:2103:25636:24158/1‑49 (MQ=14)
GGCTTTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCAT < M01420:84:000000000‑ABVEH:1:1113:12541:26187/50‑1 (MQ=33)
TTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAAC < M01420:84:000000000‑ABVEH:1:1110:12333:15667/50‑1 (MQ=33)
TTCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAAC < M01420:84:000000000‑ABVEH:1:1101:11278:23035/50‑1 (MQ=33)
TCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAACT < M01420:84:000000000‑ABVEH:1:1108:18442:13945/50‑1 (MQ=33)
TCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAACT < M01420:84:000000000‑ABVEH:1:2109:4911:13251/50‑1 (MQ=33)
TCGGCACACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAACT < M01420:84:000000000‑ABVEH:1:2110:16753:29172/50‑1 (MQ=33)
|
AGTGCTGGCCCGTTATCTGAACGAACAGCCGCAGGGCTGGCTTTCGGCGCACCGGCTGATGAAAACCCTGCGCTGGGACACAGTGCATGAACT > NC_017635/3127209‑3127301
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
