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
|
149 |
26.7 |
2337422 |
87.5% |
2045244 |
105.0 |
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%
| 96.4
/ NA
| 26 | G241G (GGA→GGC) | h16_A3001 | transcriptional regulator, LysR‑family |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (12/14); total (12/14) |
| * | AM260479 | 3,247,960 | 0 | T | A | 100.0%
| 95.0
/ NA
| 26 | F242I (TTC→ATC) | h16_A3001 | transcriptional regulator, LysR‑family |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (12/14); total (12/14) |
AACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTG > AM260479/3247834‑3248080
||
aaCTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGc > 1:291762/1‑134 (MQ=255)
ttGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGc > 2:576822/1‑134 (MQ=255)
tGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCgg < 1:849213/132‑1 (MQ=255)
aaGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGc < 1:576822/134‑1 (MQ=255)
gATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGccg < 1:103741/134‑2 (MQ=255)
ggCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACG‑GATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGccg > 2:915352/1‑123 (MQ=255)
ggCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACG‑GATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGccg < 1:915352/124‑2 (MQ=255)
aTCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAAcgt > 1:609422/1‑132 (MQ=255)
gACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGccg < 1:225040/76‑2 (MQ=255)
gACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGccg > 2:225040/1‑75 (MQ=255)
gACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACCt > 2:961413/1‑92 (MQ=255)
gACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACCt < 1:961413/92‑1 (MQ=255)
cgcgGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGc < 2:875881/134‑1 (MQ=255)
tGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAAc < 1:376193/119‑1 (MQ=255)
tGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAAc > 2:376193/1‑119 (MQ=255)
ggAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTc‑a > 1:372742/1‑122 (MQ=255)
ggAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTc‑a < 2:372742/122‑1 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGgc < 1:675650/96‑1 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGgc > 2:675650/1‑96 (MQ=255)
gaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAcc < 2:609422/134‑1 (MQ=255)
gaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAcc < 2:668196/134‑1 (MQ=255)
tCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCTGTCAAGCAGGGTGCCTACCTg > 2:176019/1‑134 (MQ=255)
cGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAc < 2:1065227/130‑1 (MQ=255)
cGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAc > 1:1065227/1‑130 (MQ=255)
gggCGTGGGCATCGTCGCCGGCGTCGCCTATGATGccg < 2:533074/38‑2 (MQ=25)
gggCGTGGGCATCGTCGCCGGCGTCGCCTATGATGccg > 1:533074/1‑37 (MQ=21)
||
AACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTG > AM260479/3247834‑3248080
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ 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
ATCACCTACGATGCCAACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATC > AM260479/3247819‑3248104
|
ATCACCTACGATGCCAACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCC > GWNJ‑0478:712:GW2002102894th:2:1201:9652:49117/1‑150 (MQ=60)
TTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGC < GWNJ‑0478:712:GW2002102894th:2:2116:8948:6685/148‑1 (MQ=60)
CAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCgagcgcgaccgcaa < GWNJ‑0478:712:GW2002102894th:2:2101:9802:16197/150‑15 (MQ=60)
AAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACG‑GATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCgagcgcgaccgcaacc < GWNJ‑0478:712:GW2002102894th:2:2202:2058:87614/150‑17 (MQ=60)
attagcgagtgtctcgtgggctcggagatgtgtataagagacagGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCgagcgcgaccgcaacc < GWNJ‑0478:712:GW2002102894th:2:1115:10738:8695/106‑17 (MQ=60)
AGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCgagcgcgaccgcaacc < GWNJ‑0478:712:GW2002102894th:2:1106:20627:46803/150‑17 (MQ=60)
gggctcggagatgtgtataagagacagGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGC < GWNJ‑0478:712:GW2002102894th:2:2209:12130:58736/122‑1 (MQ=60)
ATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTG > GWNJ‑0478:712:GW2002102894th:2:2102:15005:21620/1‑150 (MQ=60)
cggagatgtgtataagagacaGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCAC < GWNJ‑0478:712:GW2002102894th:2:2106:5565:14753/127‑1 (MQ=60)
GCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCC < GWNJ‑0478:712:GW2002102894th:2:1207:8056:77259/150‑1 (MQ=60)
GATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCT > GWNJ‑0478:712:GW2002102894th:2:1207:19100:56550/1‑149 (MQ=60)
GACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCG > GWNJ‑0478:712:GW2002102894th:2:2212:13392:26062/1‑150 (MQ=60)
CGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCgagcgcgaccgcaaccctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaatata > GWNJ‑0478:712:GW2002102894th:2:1214:9709:3789/1‑52 (MQ=60)
AGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATGCCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaacaaattgaagagctaggccacagaaca > GWNJ‑0478:712:GW2002102894th:2:2201:7448:18082/1‑47 (MQ=60)
GGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATC > GWNJ‑0478:712:GW2002102894th:2:2201:4352:100797/1‑150 (MQ=60)
|
ATCACCTACGATGCCAACTTTGCCGGCCGGACCAAGATCGACAAGGCCTTCGCGCTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATC > AM260479/3247819‑3248104
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
