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 |
3,127,458 |
C→T |
pseudogene (774/1425 nt) |
tssA → |
type VI secretion system protein TssA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,127,458 | 0 | C | T | 100.0%
| 96.6
/ NA
| 36 | pseudogene (774/1425 nt) | tssA | type VI secretion system protein TssA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (14/22); total (14/22) |
CGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGCACCGTG > NC_017635/3127413‑3127502
|
cGACCTGATGTTCAGCACTGGCGTCAGCCAATTCTGGCTGGACATTCa < 2:1988982/48‑1 (MQ=11)
gATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa > 2:1223024/1‑48 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGt < 1:1071073/46‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGt < 2:409153/46‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 2:510618/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 2:2548815/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 1:399710/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 1:320729/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 1:1360315/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 2:1950593/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTAt < 1:2133545/48‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTAt < 2:60274/48‑1 (MQ=11)
gTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCt > 2:1307723/1‑48 (MQ=11)
cAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGc < 1:1308586/47‑1 (MQ=11)
cAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGc < 2:701923/47‑1 (MQ=11)
cACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCAt > 2:2552346/1‑46 (MQ=11)
tggCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGgc > 1:108631/2‑48 (MQ=255)
tggCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGgc > 1:834998/2‑48 (MQ=255)
tggCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGgc > 1:1578480/2‑48 (MQ=255)
ggCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGgcg > 1:1441747/1‑48 (MQ=255)
cGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCt > 2:1096758/1‑48 (MQ=255)
cGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCt > 2:143318/1‑48 (MQ=255)
gTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTg < 1:24528/48‑1 (MQ=255)
gTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTg < 2:457406/48‑1 (MQ=255)
tCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGa < 1:98025/48‑1 (MQ=255)
tCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGa < 1:542391/48‑1 (MQ=255)
tCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGa < 1:2353332/48‑1 (MQ=255)
gCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACTa < 2:817335/48‑1 (MQ=255)
ctggctggACATTCAGTGGTATCTGCATCAGGCGCTGACTAAggcggg > 1:2139531/1‑48 (MQ=255)
tggctggACATTCAGTGGTATCTGCATCAGGCGCTGACTAAggcgggc > 1:1794390/1‑48 (MQ=255)
tggctggACATTCAGTGGTATCTGCATCAGGCGCTGACTAAggcgggc > 1:1709446/1‑48 (MQ=255)
gctggACATTCAGTGGTATCTGCATCAGGCGCTGACTAAggcgggcgt < 2:1106891/48‑2 (MQ=255)
ctggACATTCAGTGGTATCTGCATCAGGCGCTGACTAAggcgggcgta < 1:2514176/48‑3 (MQ=11)
ctggACATTCAGTGGTATCTGCATCAGGCGCTGACTAAggcgggcgta < 2:807523/48‑3 (MQ=11)
aCATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGTACCGt > 2:2032860/1‑48 (MQ=11)
cATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGTACCGTg > 1:1265633/1‑48 (MQ=11)
|
CGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGCACCGTG > NC_017635/3127413‑3127502
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGCACCGTGGGAC > NC_017635/3127419‑3127506
|
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCT < M01420:84:000000000‑ABVEH:1:2105:4111:8938/51‑1 (MQ=60)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATC < M01420:84:000000000‑ABVEH:1:1103:23250:21333/50‑1 (MQ=60)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATC < M01420:84:000000000‑ABVEH:1:1104:10295:14000/50‑1 (MQ=60)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATC < M01420:84:000000000‑ABVEH:1:1112:3256:17482/50‑1 (MQ=60)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTAT < M01420:84:000000000‑ABVEH:1:1110:21011:7564/49‑1 (MQ=60)
TCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCAT < M01420:84:000000000‑ABVEH:1:1112:13425:7505/50‑1 (MQ=12)
ACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCG > M01420:84:000000000‑ABVEH:1:1101:19767:26232/1‑51 (MQ=12)
ACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCG > M01420:84:000000000‑ABVEH:1:1114:11397:13501/1‑51 (MQ=12)
ACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCG > M01420:84:000000000‑ABVEH:1:1108:26857:7418/1‑51 (MQ=12)
CTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGC > M01420:84:000000000‑ABVEH:1:1113:10540:10343/1‑51 (MQ=13)
CGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGAC < M01420:84:000000000‑ABVEH:1:1101:18198:8723/51‑1 (MQ=13)
GTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACT < M01420:84:000000000‑ABVEH:1:1105:17666:19061/51‑1 (MQ=13)
GTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACT < M01420:84:000000000‑ABVEH:1:1101:21671:23484/51‑1 (MQ=13)
GTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACT < M01420:84:000000000‑ABVEH:1:2107:19730:6072/51‑1 (MQ=13)
TTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGG > M01420:84:000000000‑ABVEH:1:2105:10452:10177/1‑51 (MQ=13)
TCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCG > M01420:84:000000000‑ABVEH:1:2101:25986:15865/1‑51 (MQ=13)
TCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCG > M01420:84:000000000‑ABVEH:1:2102:11692:10042/1‑51 (MQ=13)
TCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGC < M01420:84:000000000‑ABVEH:1:2112:24938:14223/50‑1 (MQ=13)
GGCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGTAC < M01420:84:000000000‑ABVEH:1:2111:24318:16773/51‑1 (MQ=12)
GCTGGACATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGTACC < M01420:84:000000000‑ABVEH:1:2108:7887:14619/51‑1 (MQ=12)
GACATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGTACCGTGG > M01420:84:000000000‑ABVEH:1:1111:12305:22359/1‑51 (MQ=0)
ATTCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGTACCGTGGGAC > M01420:84:000000000‑ABVEH:1:2104:21783:18262/1‑51 (MQ=0)
|
GATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGGCGCTGACTAAGGCGGGCGCACCGTGGGAC > NC_017635/3127419‑3127506
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
