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 |
3,053,299 |
(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%
| 92.7
/ NA
| 24 | intergenic (‑24/‑294) | ygcW/yqcE | SDR family oxidoreductase/MFS transporter |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base A (9/15); total (9/15) |
TGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGG > NC_017635/3053249‑3053325
|
tGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaa > 1:1089375/1‑47 (MQ=255)
tGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaa > 2:33451/1‑47 (MQ=255)
tGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaa > 2:1119251/1‑47 (MQ=255)
agagaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaa < 2:978787/48‑1 (MQ=255)
gagaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaa > 1:1977074/1‑47 (MQ=255)
gagaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaa > 1:333465/1‑47 (MQ=255)
agaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaa > 1:2309344/1‑46 (MQ=255)
gaTTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑aaaaaaaaag < 1:2436029/48‑3 (MQ=255)
gATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAaaagaaag < 1:1218030/47‑1 (MQ=255)
gATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAgg < 2:1067414/48‑1 (MQ=255)
gATTGACATAGTTAGATCCAATTTCCGTAAGGCAAAAAAAAAGAAAgg > 1:1189014/1‑48 (MQ=38)
ttGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGt > 1:2526349/1‑47 (MQ=255)
ttGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTa < 1:707732/48‑1 (MQ=255)
ttGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTa < 2:2216226/48‑1 (MQ=255)
ttGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTa < 1:870952/48‑1 (MQ=255)
ttGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTa < 1:39865/48‑1 (MQ=255)
ttGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTa < 1:1539393/48‑1 (MQ=255)
gACATAGTTAGCTTCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTaa < 2:272441/47‑1 (MQ=37)
gACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTaa < 2:2053229/47‑1 (MQ=255)
gACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTaa < 1:1492708/47‑1 (MQ=255)
gACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTaa < 2:2260469/47‑1 (MQ=255)
aCATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAAc < 2:30940/47‑1 (MQ=255)
aGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccc > 1:608666/1‑48 (MQ=38)
aGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccc > 1:861146/1‑48 (MQ=38)
aGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccc > 1:420375/1‑48 (MQ=38)
aGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccc > 2:457307/1‑48 (MQ=38)
aGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccc > 2:1895956/1‑48 (MQ=38)
aGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccc > 2:1980154/1‑48 (MQ=38)
gTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTccc < 1:1035228/47‑1 (MQ=38)
aGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCcg < 1:149055/47‑1 (MQ=38)
gCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCcgcg < 2:1775285/48‑1 (MQ=38)
tttCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAggg > 1:1180201/1‑47 (MQ=38)
|
TGAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGG > NC_017635/3053249‑3053325
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ 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
GAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTATCTCTG > NC_017635/3053250‑3053349
|
GAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAA > M01420:84:000000000‑ABVEH:1:2103:19077:23516/1‑50 (MQ=60)
GAGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAA > M01420:84:000000000‑ABVEH:1:1103:8296:24131/1‑50 (MQ=60)
AGAGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGC‑AAAAAAAA > M01420:84:000000000‑ABVEH:1:2106:27467:20601/1‑49 (MQ=60)
AGATTCGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAA < M01420:84:000000000‑ABVEH:1:2107:8178:22343/51‑1 (MQ=60)
TCGATTGACATAGTTAGATCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGT > M01420:84:000000000‑ABVEH:1:1111:26979:7403/1‑51 (MQ=54)
CGATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGT < M01420:84:000000000‑ABVEH:1:1111:22376:13208/50‑1 (MQ=60)
GATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTA > M01420:84:000000000‑ABVEH:1:2108:15813:16914/1‑50 (MQ=60)
ATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAAC < M01420:84:000000000‑ABVEH:1:1101:15432:11850/51‑1 (MQ=60)
ATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAAC < M01420:84:000000000‑ABVEH:1:1114:9344:5470/51‑1 (MQ=60)
ATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAAC < M01420:84:000000000‑ABVEH:1:1108:13306:14650/51‑1 (MQ=60)
ATTGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAAC < M01420:84:000000000‑ABVEH:1:1107:20745:5023/51‑1 (MQ=60)
TGACATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACT < M01420:84:000000000‑ABVEH:1:1113:16903:19907/50‑1 (MQ=60)
CATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCC < M01420:84:000000000‑ABVEH:1:2110:16112:11845/51‑1 (MQ=60)
ATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCC > M01420:84:000000000‑ABVEH:1:1108:9469:12771/1‑51 (MQ=60)
ATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCC > M01420:84:000000000‑ABVEH:1:1106:26283:9230/1‑51 (MQ=60)
ATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCC > M01420:84:000000000‑ABVEH:1:1104:12459:17970/1‑51 (MQ=60)
ATAGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCC > M01420:84:000000000‑ABVEH:1:2113:3680:19223/1‑51 (MQ=60)
AGTTAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCC < M01420:84:000000000‑ABVEH:1:1109:24493:23920/50‑1 (MQ=60)
TAGCTCCAATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCG < M01420:84:000000000‑ABVEH:1:1102:25540:10498/50‑1 (MQ=60)
AATTTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGA > M01420:84:000000000‑ABVEH:1:1111:12772:5299/1‑50 (MQ=60)
TTCCGTAAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTT > M01420:84:000000000‑ABVEH:1:2113:7499:11542/1‑51 (MQ=60)
AAGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTT < M01420:84:000000000‑ABVEH:1:2112:22166:11993/50‑1 (MQ=60)
AGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTC > M01420:84:000000000‑ABVEH:1:2104:20375:27445/1‑51 (MQ=60)
AGGCAAAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTC > M01420:84:000000000‑ABVEH:1:2101:24750:23989/1‑51 (MQ=60)
A‑AAAAAAAAGAAAGGTAACTTTCCCCGCGAGAGGGAAGTTACCTTTCTCAT > M01420:84:000000000‑ABVEH:1:2106:20057:19618/1‑51 (MQ=60)
AAAAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATT < M01420:84:000000000‑ABVEH:1:2102:11008:11474/51‑1 (MQ=60)
AAAAAAGAAAGGTAACTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTAT < M01420:84:000000000‑ABVEH:1:1102:28813:14193/51‑1 (MQ=60)
AGAAAGGTATCTTCCCCCGCGAGAGGGAAGTTACCTTTCTCATTATCTCTG < M01420:84:000000000‑ABVEH:1:2109:5879:12702/51‑1 (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 < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
