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 |
3,750,975 |
G→A |
intergenic (‑108/‑504) |
malP ← / → malT |
maltodextrin phosphorylase/HTH‑type transcriptional regulator MalT |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,750,975 | 0 | G | A | 100.0%
| 161.9
/ NA
| 40 | intergenic (‑108/‑504) | malP/malT | maltodextrin phosphorylase/HTH‑type transcriptional regulator MalT |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (23/17); total (23/17) |
ACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAA > NC_017635/3750932‑3751019
|
aCCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGAt > 1:238692/1‑47 (MQ=255)
aCCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGAt > 2:1497326/1‑47 (MQ=255)
cTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAg < 2:1004366/48‑1 (MQ=255)
ccTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGc > 2:817473/1‑46 (MQ=255)
cTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg > 1:992022/1‑48 (MQ=255)
aTCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAgg < 1:1699160/46‑1 (MQ=255)
tCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGaaa > 2:788574/1‑48 (MQ=255)
cGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAtgtg < 1:2324805/47‑1 (MQ=255)
cGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGa < 2:857640/48‑1 (MQ=255)
cGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGa < 2:689974/48‑1 (MQ=255)
cGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGa < 1:877808/48‑1 (MQ=255)
cGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGa < 2:1965623/48‑1 (MQ=255)
ggggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtc < 2:2454352/48‑1 (MQ=255)
gggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct > 2:2585746/1‑48 (MQ=255)
gggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct > 1:805513/1‑48 (MQ=255)
gggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct < 2:362270/48‑1 (MQ=255)
gATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCa < 2:1126781/48‑1 (MQ=255)
aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCaa > 1:623610/1‑48 (MQ=255)
ttAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc > 2:452369/1‑48 (MQ=255)
ttAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc > 2:1419373/1‑48 (MQ=255)
tAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc > 2:1063395/1‑47 (MQ=255)
tAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc > 2:437331/1‑47 (MQ=255)
tAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc > 1:766505/1‑47 (MQ=255)
tAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc > 1:1478952/1‑47 (MQ=255)
ggCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAcctc < 2:1192171/48‑3 (MQ=255)
gCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACt > 2:1438942/1‑48 (MQ=255)
gCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACt > 2:413256/1‑48 (MQ=255)
cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACtt < 2:1410086/48‑1 (MQ=255)
ggaggaGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:119561/1‑46 (MQ=255)
ggaggaGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:2457073/1‑46 (MQ=255)
ggaggaGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:1468835/1‑46 (MQ=255)
ggaggaGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa > 1:2195947/1‑46 (MQ=255)
gaggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAg < 1:2621798/48‑1 (MQ=255)
gaggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAg < 1:2557268/48‑1 (MQ=255)
gaggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAg < 2:257435/48‑1 (MQ=255)
gaggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAg > 1:1658781/1‑48 (MQ=255)
ggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGc > 1:1544548/1‑47 (MQ=255)
ggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCt < 2:344973/48‑1 (MQ=255)
agTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAg > 1:2203138/1‑48 (MQ=255)
cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCaa < 1:1385415/48‑1 (MQ=255)
|
ACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAA > NC_017635/3750932‑3751019
|
| 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
GTTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACCAC > NC_017635/3750928‑3751024
|
GTTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGAT < M01420:84:000000000‑ABVEH:1:1113:18687:17900/51‑1 (MQ=60)
TGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATG > M01420:84:000000000‑ABVEH:1:1103:21741:4420/1‑50 (MQ=60)
TCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGG > M01420:84:000000000‑ABVEH:1:1109:7678:15274/1‑51 (MQ=60)
CATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAA < M01420:84:000000000‑ABVEH:1:2101:26186:13894/49‑1 (MQ=60)
GCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATC < M01420:84:000000000‑ABVEH:1:1108:21400:15966/51‑1 (MQ=60)
GCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATC < M01420:84:000000000‑ABVEH:1:2110:14261:5577/51‑1 (MQ=60)
GCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAT < M01420:84:000000000‑ABVEH:1:2106:26590:23995/50‑1 (MQ=60)
GGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTC > M01420:84:000000000‑ABVEH:1:1107:7702:25260/1‑51 (MQ=60)
GGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAC > M01420:84:000000000‑ABVEH:1:1106:10733:12223/1‑51 (MQ=60)
ATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACC > M01420:84:000000000‑ABVEH:1:1107:12164:17085/1‑50 (MQ=60)
ATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACC > M01420:84:000000000‑ABVEH:1:1113:10399:17301/1‑50 (MQ=60)
AGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTT > M01420:84:000000000‑ABVEH:1:2110:20229:12147/1‑51 (MQ=60)
AGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:84:000000000‑ABVEH:1:1113:18749:15433/1‑49 (MQ=60)
AGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:84:000000000‑ABVEH:1:2107:21261:28176/1‑49 (MQ=60)
AGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:84:000000000‑ABVEH:1:1102:22010:3378/1‑49 (MQ=60)
AGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAA > M01420:84:000000000‑ABVEH:1:2105:24337:21113/1‑49 (MQ=60)
GGGAGGAGTTGCTGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGC > M01420:84:000000000‑ABVEH:1:2111:22622:11921/1‑51 (MQ=60)
GGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGC > M01420:84:000000000‑ABVEH:1:2101:10416:5340/1‑51 (MQ=60)
GGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCT < M01420:84:000000000‑ABVEH:1:2108:9571:22979/51‑1 (MQ=60)
GGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCT < M01420:84:000000000‑ABVEH:1:2109:21519:12473/51‑1 (MQ=60)
GAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCT > M01420:84:000000000‑ABVEH:1:1114:23156:6701/1‑50 (MQ=60)
GGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGT > M01420:84:000000000‑ABVEH:1:2105:17910:22694/1‑51 (MQ=60)
GCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAC < M01420:84:000000000‑ABVEH:1:1112:14020:22414/51‑1 (MQ=60)
GAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACCAC > M01420:84:000000000‑ABVEH:1:2103:27701:10170/1‑51 (MQ=60)
GAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACCAC < M01420:84:000000000‑ABVEH:1:2110:3857:20401/51‑1 (MQ=60)
GAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACCAC < M01420:84:000000000‑ABVEH:1:1111:18724:16937/51‑1 (MQ=60)
|
GTTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAACCAC > NC_017635/3750928‑3751024
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
