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 |
|
A0 F0 I1 R1
|
146 |
27.9 |
2327082 |
89.7% |
2087392 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,247,959 |
2 bp→CA |
coding (723‑724/813 nt) |
h16_A3001 → |
transcriptional regulator, LysR‑family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,247,959 | 0 | A | C | 100.0%
| 82.6
/ NA
| 22 | G241G (GGA→GGC) | h16_A3001 | transcriptional regulator, LysR‑family |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (8/14); total (8/14) |
| * | AM260479 | 3,247,960 | 0 | T | A | 100.0%
| 81.9
/ NA
| 22 | F242I (TTC→ATC) | h16_A3001 | transcriptional regulator, LysR‑family |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (8/14); total (8/14) |
ACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTT > AM260479/3247835‑3248088
||
aCTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGcc < 1:153991/134‑1 (MQ=255)
aCTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGcc < 2:583338/134‑1 (MQ=255)
aCTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGcc < 2:32534/134‑1 (MQ=255)
aCTTTGCCGGCCGGACCAAGATCGACAAGGCCTCCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGcc > 2:1093797/1‑134 (MQ=255)
tGCCGGCCGGACCAAGATCTACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCgg < 1:824543/132‑1 (MQ=255)
aCAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGccgagcgc > 2:310863/1‑128 (MQ=255)
aGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggcc < 1:94936/134‑1 (MQ=255)
aGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggcc < 1:27629/134‑1 (MQ=255)
aGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGgcag > 1:2694/1‑133 (MQ=255)
gACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggccgg < 1:337057/110‑1 (MQ=255)
gACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggccgg > 2:337057/1‑110 (MQ=255)
tCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTc < 1:1093797/134‑1 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggcc < 2:792981/81‑1 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggcc < 2:612166/81‑1 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggcc > 1:792981/1‑81 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggcc > 1:612166/1‑81 (MQ=255)
ggCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCt < 1:692705/106‑1 (MQ=255)
ggCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCt > 2:692705/1‑106 (MQ=255)
ggCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTgcgc < 2:2694/134‑1 (MQ=255)
ggCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTgcg > 2:1125456/1‑133 (MQ=255)
ggCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCtt < 1:310863/134‑1 (MQ=255)
gTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTgcgc < 2:253968/126‑1 (MQ=255)
||
ACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTT > AM260479/3247835‑3248088
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
GCTGATCACCTACGATGCCAACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCAT > AM260479/3247815‑3248103
|
GCTGATCACCTACGATGCCAACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGT < GWNJ‑0478:712:GW2002102894th:2:2111:13496:11056/150‑1 (MQ=60)
AACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGAT < GWNJ‑0478:712:GW2002102894th:2:1111:2399:15454/150‑1 (MQ=60)
TTGCCGGCCGGACCAAGATCTACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGC < GWNJ‑0478:712:GW2002102894th:2:2115:15516:74878/148‑1 (MQ=60)
GACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCgagcgcgaccg > GWNJ‑0478:712:GW2002102894th:2:1216:7171:89106/1‑139 (MQ=60)
GGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCgagcgcgaccgcaacctgcgcggcat > GWNJ‑0478:712:GW2002102894th:2:1212:11276:49175/1‑124 (MQ=60)
GAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGC < GWNJ‑0478:712:GW2002102894th:2:1103:3239:75787/150‑1 (MQ=60)
GAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGC < GWNJ‑0478:712:GW2002102894th:2:1107:10622:81627/150‑1 (MQ=60)
aagagacagGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAG < GWNJ‑0478:712:GW2002102894th:2:1205:3669:14435/140‑1 (MQ=60)
CGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGC > GWNJ‑0478:712:GW2002102894th:2:1101:7987:19233/1‑149 (MQ=60)
gtataagagacagCGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGG < GWNJ‑0478:712:GW2002102894th:2:2106:13122:77887/136‑1 (MQ=60)
ATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCctgtctcttatacacatctccgagcccacgagacactcg > GWNJ‑0478:712:GW2002102894th:2:2112:13925:16481/1‑111 (MQ=60)
ATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCctgtctcttatacacatctccgagcccacgagacactcg > GWNJ‑0478:712:GW2002102894th:2:2103:20064:84408/1‑111 (MQ=60)
ATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAC < GWNJ‑0478:712:GW2002102894th:2:2213:4625:70100/150‑1 (MQ=60)
GAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTC > GWNJ‑0478:712:GW2002102894th:2:1114:10031:30035/1‑150 (MQ=60)
AGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaataccactatacacggatacgcagcacc > GWNJ‑0478:712:GW2002102894th:2:1102:1726:51472/1‑47 (MQ=60)
GATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCgagcgcgaccgcaacctgcgcgctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1102:14074:40094/1‑46 (MQ=60)
GGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCAT < GWNJ‑0478:712:GW2002102894th:2:1203:17456:52671/150‑1 (MQ=60)
|
GCTGATCACCTACGATGCCAACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCAT > AM260479/3247815‑3248103
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
