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
|
61 |
39.0 |
4165548 |
97.4% |
4057243 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,053,299 |
(A)8→9 |
intergenic (‑32/‑286) |
ygcW ← / → yqcE |
SDR family oxidoreductase/MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,053,291 | 1 | . | A | 100.0%
| 134.6
/ NA
| 37 | intergenic (‑24/‑294) | ygcW/yqcE | SDR family oxidoreductase/MFS transporter |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base A (17/20); total (17/20) |
AACGCATTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCT > NC_017635/3053242‑3053334
|
aaCGCATTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGc < 2:1810405/50‑1 (MQ=255)
aCGCATTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGc > 1:1075239/1‑49 (MQ=255)
cGCATTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aa < 1:1058007/50‑1 (MQ=255)
cGCATTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑a > 1:1704265/1‑49 (MQ=255)
gCATTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaa < 2:338873/50‑1 (MQ=255)
gCATTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aa > 1:2062774/1‑49 (MQ=255)
aTTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaa > 2:288765/1‑49 (MQ=255)
aTTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGGAAGGC‑aaaa > 1:2034919/1‑49 (MQ=255)
ttGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaa > 1:1734688/1‑49 (MQ=255)
ttGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaa > 1:509582/1‑49 (MQ=255)
tGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaa > 2:1295178/1‑49 (MQ=255)
tGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaa > 1:1894099/1‑49 (MQ=255)
gagagaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaa > 1:1091445/1‑49 (MQ=255)
gagagaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaa < 1:407119/49‑1 (MQ=255)
agagaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaa > 2:1399527/1‑48 (MQ=255)
agaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaaaag > 1:648616/1‑47 (MQ=255)
agaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaaaag > 2:1077418/1‑47 (MQ=255)
ttCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAaaagaaag > 1:988114/1‑50 (MQ=255)
ttCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAaaagaaag < 1:1750557/50‑1 (MQ=255)
ttCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAaaagaaag < 2:441617/50‑1 (MQ=255)
tCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAgg > 2:1398582/1‑50 (MQ=255)
tCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAgg > 1:428093/1‑50 (MQ=255)
cGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAgg < 2:554192/49‑1 (MQ=255)
gATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGt > 1:218107/1‑49 (MQ=255)
gATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTa < 1:1241354/50‑1 (MQ=255)
aTTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTaa > 2:1767462/1‑50 (MQ=255)
aTTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTaa < 1:1030315/50‑1 (MQ=255)
tGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACt > 1:1342899/1‑50 (MQ=255)
gACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACt < 1:1613297/49‑1 (MQ=255)
cATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcc < 2:269449/50‑1 (MQ=255)
cATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcc > 2:274066/1‑50 (MQ=255)
cATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcc < 1:314929/50‑1 (MQ=255)
cATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcc < 1:1913649/50‑1 (MQ=255)
cATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcc < 2:716128/50‑1 (MQ=255)
cATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcc > 2:786171/1‑50 (MQ=255)
cATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcc < 2:1920647/50‑1 (MQ=255)
aTAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccc < 2:60940/50‑1 (MQ=39)
tAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcccc < 2:676825/50‑1 (MQ=39)
tAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTcccc < 1:1636614/50‑1 (MQ=39)
aGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccccc > 2:88946/1‑50 (MQ=39)
aGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccccc > 1:696362/1‑50 (MQ=39)
ttAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCcgc < 2:1476972/50‑1 (MQ=39)
ttAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCcgc < 2:446523/50‑1 (MQ=39)
aGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCcgc > 2:1189195/1‑48 (MQ=38)
cTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCga > 1:948945/1‑48 (MQ=38)
cAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAggg < 1:749859/50‑1 (MQ=39)
cAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAggg < 1:1798185/50‑1 (MQ=39)
aTTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAggg > 1:2025374/1‑48 (MQ=38)
aTTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAggg > 1:1161830/1‑48 (MQ=38)
aTTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGaa < 1:1646397/50‑1 (MQ=38)
cGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTAc > 1:346534/1‑50 (MQ=37)
tAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCt > 2:256657/1‑50 (MQ=25)
tAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCt < 1:998280/50‑1 (MQ=25)
tAAGGCAAAAAAAAAGAAAGGAAACTTCCCCCGCGAGAGGGAAGTTACCt > 2:1804059/1‑50 (MQ=25)
|
AACGCATTGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCT > NC_017635/3053242‑3053334
|
| 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
GAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTATCTCTG > NC_017635/3053250‑3053349
|
GAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAA > M01420:85:000000000‑AC936:1:2101:12139:22026/1‑50 (MQ=60)
AGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAAaga > M01420:85:000000000‑AC936:1:1109:16463:21221/1‑47 (MQ=60)
ATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAG < M01420:85:000000000‑AC936:1:2110:4404:19163/51‑1 (MQ=60)
TTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGG > M01420:85:000000000‑AC936:1:1114:17783:12817/1‑51 (MQ=60)
TCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGT > M01420:85:000000000‑AC936:1:1106:11915:21083/1‑51 (MQ=60)
CGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTA < M01420:85:000000000‑AC936:1:2103:6789:22999/51‑1 (MQ=60)
GATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAA < M01420:85:000000000‑AC936:1:1114:11407:26693/51‑1 (MQ=60)
GATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTA > M01420:85:000000000‑AC936:1:1103:21026:25947/1‑50 (MQ=60)
TGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTT > M01420:85:000000000‑AC936:1:2105:7880:8524/1‑51 (MQ=60)
TGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACT < M01420:85:000000000‑AC936:1:2108:9216:23311/50‑1 (MQ=60)
ACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCC < M01420:85:000000000‑AC936:1:1105:16365:9439/51‑1 (MQ=60)
ACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCC < M01420:85:000000000‑AC936:1:2112:16095:22696/51‑1 (MQ=60)
ATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCC < M01420:85:000000000‑AC936:1:2109:15775:7462/51‑1 (MQ=60)
AGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCG > M01420:85:000000000‑AC936:1:1110:10572:13483/1‑51 (MQ=60)
CTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAG > M01420:85:000000000‑AC936:1:1113:16813:23558/1‑49 (MQ=60)
CCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGG < M01420:85:000000000‑AC936:1:2111:10249:10999/51‑1 (MQ=60)
CCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGG < M01420:85:000000000‑AC936:1:1111:4703:7141/51‑1 (MQ=60)
AATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAA < M01420:85:000000000‑AC936:1:2109:17188:10657/51‑1 (MQ=60)
ATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGA > M01420:85:000000000‑AC936:1:2102:28113:21150/1‑49 (MQ=60)
ATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGA > M01420:85:000000000‑AC936:1:2114:13298:10092/1‑49 (MQ=60)
CGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACC > M01420:85:000000000‑AC936:1:1105:2420:18817/1‑51 (MQ=60)
GTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCT < M01420:85:000000000‑AC936:1:1114:9320:15802/51‑1 (MQ=60)
AAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTT < M01420:85:000000000‑AC936:1:1102:12173:17597/50‑1 (MQ=60)
AAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTT < M01420:85:000000000‑AC936:1:1113:16426:19856/50‑1 (MQ=60)
AAGGCAAAAAAAAAGAAAGGTAACGTCCCCCGCGAGAGGGAAGTTACCTT < M01420:85:000000000‑AC936:1:2103:17389:1856/50‑1 (MQ=59)
AGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTC < M01420:85:000000000‑AC936:1:1109:25666:21220/51‑1 (MQ=60)
gcaAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTC < M01420:85:000000000‑AC936:1:1110:8004:6471/48‑1 (MQ=60)
A‑AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCAT > M01420:85:000000000‑AC936:1:2105:18829:3593/1‑51 (MQ=60)
AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATT > M01420:85:000000000‑AC936:1:2107:20035:19701/1‑51 (MQ=60)
AAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTA < M01420:85:000000000‑AC936:1:1107:8077:18726/51‑1 (MQ=60)
AAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTA < M01420:85:000000000‑AC936:1:1101:5614:5755/51‑1 (MQ=60)
AAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATT > M01420:85:000000000‑AC936:1:2103:22772:26043/1‑50 (MQ=60)
AAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATT > M01420:85:000000000‑AC936:1:1114:26195:24514/1‑50 (MQ=60)
AAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATT > M01420:85:000000000‑AC936:1:1104:20825:21417/1‑50 (MQ=60)
AAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTATCTC < M01420:85:000000000‑AC936:1:2105:10429:26324/51‑1 (MQ=60)
AGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTATCTCTG < M01420:85:000000000‑AC936:1:1114:17522:24034/51‑1 (MQ=60)
|
GAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTATCTCTG > NC_017635/3053250‑3053349
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
