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 |
3,655,775 |
G→A |
S431F (TCT→TTT) |
secY ← |
preprotein translocase subunit SecY |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,655,775 | 0 | G | A | 100.0%
| 214.6
/ NA
| 55 | S431F (TCT→TTT) | secY | preprotein translocase subunit SecY |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (9/46); total (9/46) |
ACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAGACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCAT > NC_017635/3655730‑3655818
|
aCCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAAc < 2:1683953/48‑1 (MQ=255)
aCCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAAc < 1:935058/48‑1 (MQ=255)
cAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACt > 1:713488/1‑47 (MQ=255)
cAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTc < 2:2607533/48‑1 (MQ=255)
cAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTc < 2:1639449/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 1:1068538/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:862885/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:811612/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:423021/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:208326/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:1997301/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:193161/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:1689438/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:1686025/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:1114286/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 2:1079077/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 1:1564206/48‑1 (MQ=255)
aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 1:228588/48‑1 (MQ=255)
aTTAGCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt < 1:110634/48‑1 (MQ=38)
ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATa < 1:246751/48‑1 (MQ=255)
ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATa < 2:2428735/48‑1 (MQ=255)
ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATa < 2:1306481/48‑1 (MQ=255)
ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATa < 2:563831/48‑1 (MQ=255)
ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATa < 1:656161/48‑1 (MQ=255)
ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATa < 1:106627/48‑1 (MQ=255)
ggCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactga < 2:2319242/47‑1 (MQ=255)
ggCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactga < 2:2408948/47‑1 (MQ=255)
ggCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactga < 2:1144372/47‑1 (MQ=255)
gCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgact < 1:2416986/48‑1 (MQ=255)
gCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgact < 2:789655/48‑1 (MQ=255)
cGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTgg < 1:2159220/48‑1 (MQ=255)
cGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTgg < 1:388857/48‑1 (MQ=255)
tAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAc < 1:1558279/48‑1 (MQ=255)
tAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAc < 2:809608/48‑1 (MQ=255)
ccTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAcatc < 2:1390649/48‑1 (MQ=255)
ccTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAcatc < 1:882337/48‑1 (MQ=255)
tCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACatcatc < 1:2484020/47‑1 (MQ=255)
cAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACAtcatca < 2:606699/47‑1 (MQ=255)
aGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCaga < 1:1706692/48‑1 (MQ=255)
ggTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCagag > 1:641318/1‑48 (MQ=255)
cGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGttt < 1:1298511/47‑1 (MQ=255)
gCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGc < 1:964170/48‑1 (MQ=255)
ccTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCa > 1:2042310/1‑48 (MQ=255)
cttcttCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCAc < 1:1376023/48‑1 (MQ=255)
cttcttCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCAc < 1:1330342/48‑1 (MQ=255)
cttcAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACtt > 1:1758473/1‑47 (MQ=255)
cttcAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACtt > 1:2060388/1‑47 (MQ=255)
tcAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAg > 2:76637/1‑48 (MQ=255)
aaTGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc < 1:1577334/48‑1 (MQ=255)
aaTGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc < 2:1680539/48‑1 (MQ=255)
aaTGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGc < 2:1568908/47‑1 (MQ=255)
aTGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCa < 2:1980000/48‑1 (MQ=255)
aTGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCa > 1:1080907/1‑48 (MQ=255)
tGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCa > 2:1278082/1‑47 (MQ=255)
gCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGTCAt > 2:8912/1‑47 (MQ=255)
|
ACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAGACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCAT > NC_017635/3655730‑3655818
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGGCGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAGACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAAAGT > NC_017635/3655725‑3655823
|
GGGCGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAA < M01420:84:000000000‑ABVEH:1:2114:28236:20368/51‑1 (MQ=60)
GGCGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAA < M01420:84:000000000‑ABVEH:1:1104:19716:17080/51‑1 (MQ=60)
GCGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAAC < M01420:84:000000000‑ABVEH:1:2101:4919:22776/51‑1 (MQ=60)
GACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTC < M01420:84:000000000‑ABVEH:1:1109:17562:2473/51‑1 (MQ=60)
ACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTC > M01420:84:000000000‑ABVEH:1:1107:14713:6463/1‑50 (MQ=60)
AATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATAC < M01420:84:000000000‑ABVEH:1:1102:9447:27570/51‑1 (MQ=60)
AATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATAC < M01420:84:000000000‑ABVEH:1:2113:27191:13163/51‑1 (MQ=60)
AATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATAC > M01420:84:000000000‑ABVEH:1:2112:7301:26114/1‑51 (MQ=60)
AATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATAC < M01420:84:000000000‑ABVEH:1:1114:28159:10778/51‑1 (MQ=60)
AATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATAC < M01420:84:000000000‑ABVEH:1:1110:22148:6986/51‑1 (MQ=60)
AATTAGCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATAC < M01420:84:000000000‑ABVEH:1:1101:13942:26873/51‑1 (MQ=60)
ATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACT < M01420:84:000000000‑ABVEH:1:1101:21265:25641/51‑1 (MQ=60)
ATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACT < M01420:84:000000000‑ABVEH:1:2112:15227:10849/51‑1 (MQ=60)
ATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACT < M01420:84:000000000‑ABVEH:1:1103:23991:6540/51‑1 (MQ=60)
ATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACT < M01420:84:000000000‑ABVEH:1:1106:20328:18451/51‑1 (MQ=60)
GGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGG < M01420:84:000000000‑ABVEH:1:2107:16238:18552/51‑1 (MQ=60)
CCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAC < M01420:84:000000000‑ABVEH:1:1104:28996:11866/51‑1 (MQ=60)
CCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAC < M01420:84:000000000‑ABVEH:1:2105:5307:14014/51‑1 (MQ=60)
GTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACAT > M01420:84:000000000‑ABVEH:1:2112:7768:12171/1‑51 (MQ=60)
GTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACAT < M01420:84:000000000‑ABVEH:1:1114:16409:9619/51‑1 (MQ=60)
GCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCAT < M01420:84:000000000‑ABVEH:1:1108:20202:16818/51‑1 (MQ=60)
TTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAG < M01420:84:000000000‑ABVEH:1:2108:11594:8843/50‑1 (MQ=60)
CAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGT < M01420:84:000000000‑ABVEH:1:2101:21132:15340/51‑1 (MQ=60)
CAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGT > M01420:84:000000000‑ABVEH:1:1106:2342:15572/1‑51 (MQ=60)
AGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTT > M01420:84:000000000‑ABVEH:1:2113:10418:9819/1‑51 (MQ=60)
GGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTT < M01420:84:000000000‑ABVEH:1:2111:14487:25820/51‑1 (MQ=60)
TCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGC < M01420:84:000000000‑ABVEH:1:1112:19309:5052/50‑1 (MQ=60)
CGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCAC < M01420:84:000000000‑ABVEH:1:1109:28635:9937/51‑1 (MQ=60)
CGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCAC > M01420:84:000000000‑ABVEH:1:2104:13687:13611/1‑51 (MQ=60)
CCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTT < M01420:84:000000000‑ABVEH:1:1112:9058:11878/51‑1 (MQ=60)
CCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTT < M01420:84:000000000‑ABVEH:1:1112:13153:20507/51‑1 (MQ=60)
TTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTG > M01420:84:000000000‑ABVEH:1:2104:2404:17023/1‑50 (MQ=60)
TTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTG > M01420:84:000000000‑ABVEH:1:2101:11918:26563/1‑50 (MQ=60)
TCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTG < M01420:84:000000000‑ABVEH:1:2109:8354:16968/49‑1 (MQ=60)
CAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCAT < M01420:84:000000000‑ABVEH:1:1114:10073:13285/51‑1 (MQ=60)
CAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCAT > M01420:84:000000000‑ABVEH:1:1110:26052:9606/1‑51 (MQ=60)
GCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAAAG < M01420:84:000000000‑ABVEH:1:2102:22132:11497/51‑1 (MQ=60)
GCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAAA < M01420:84:000000000‑ABVEH:1:1104:13469:18849/50‑1 (MQ=60)
GCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAA > M01420:84:000000000‑ABVEH:1:2102:22152:18239/1‑49 (MQ=60)
CAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAAAGT < M01420:84:000000000‑ABVEH:1:1113:19442:28716/51‑1 (MQ=60)
CAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAAAGT < M01420:84:000000000‑ABVEH:1:1107:9941:16520/51‑1 (MQ=60)
|
GGGCGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAGACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAAAGT > NC_017635/3655725‑3655823
|
| 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: ‑ |
