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 |
3,375,228 |
(T)7→8 |
coding (2219/2220 nt) |
ygiQ ← |
YgiQ family radical SAM protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,375,221 | 1 | . | T | 94.1%
| 57.8
/ ‑3.2
| 17 | intergenic (+36/+6) | yqhH/ygiQ | lipoprotein YqhH/YgiQ family radical SAM protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (10/6); total (10/7) |
| Fisher's exact test for biased strand distribution p-value = 4.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCGTTTCTTCGC > NC_017635/3375174‑3375262
|
tACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGa < 1:1030687/48‑1 (MQ=255)
cGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑t < 2:439884/47‑1 (MQ=255)
gCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑ttt > 2:464494/1‑48 (MQ=255)
aaTGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑ttttttt > 1:2294019/1‑48 (MQ=255)
aaTGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑ttttttt > 2:1991011/1‑48 (MQ=255)
aaTGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑ttttttt > 2:1098500/1‑48 (MQ=255)
aTGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑ttttttt > 2:670938/1‑47 (MQ=255)
aTGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑ttttttt > 1:652382/1‑47 (MQ=255)
tGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑tttttttta < 1:494118/48‑3 (MQ=255)
tGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑tttttttt > 1:946738/1‑46 (MQ=255)
aaaaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACGt < 2:229891/47‑1 (MQ=37)
aaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACGTCCaa < 2:1034703/48‑1 (MQ=38)
aaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACGTCCaa < 2:205525/48‑1 (MQ=38)
agcaTGTCAGTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCtt > 2:2307902/1‑46 (MQ=38)
gTCAGTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCg > 1:2033250/1‑48 (MQ=38)
gTCAGTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCg > 2:1595613/1‑48 (MQ=38)
gTCAGTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCg > 2:1982260/1‑48 (MQ=38)
gTCAGTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCg > 1:72868/1‑48 (MQ=38)
gTCAGTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCg > 1:342125/1‑48 (MQ=38)
gTCAGTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCg > 2:433749/1‑48 (MQ=38)
tCAGTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCGt < 2:2103650/48‑1 (MQ=38)
aGTGGCCGGGGA‑TTTTTTTAAACGTCCAACCGCCGCTTTAGGGCGttt < 2:2265120/48‑1 (MQ=37)
gTTGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCGTttc > 2:1276708/1‑48 (MQ=38)
ttGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCGTttct > 2:1053344/1‑48 (MQ=38)
tggCCGGGGTTTTTTTTT‑ACCGTCCAACCGCCGCTTTAGGGCGTttct < 1:1458253/46‑1 (MQ=25)
tGCCGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCGTttctt > 2:2100496/1‑48 (MQ=38)
cGGGGATTTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCGTTTCTTCGc < 2:147501/48‑1 (MQ=39)
|
TACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTT‑AACGTCCAACCGCCGCTTTAGGGCGTTTCTTCGC > NC_017635/3375174‑3375262
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ 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
AGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTTAACGTCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACCGG > NC_017635/3375179‑3375277
|
AGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTTT > M01420:84:000000000‑ABVEH:1:2106:18235:17589/1‑51 (MQ=60)
GAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTTT > M01420:84:000000000‑ABVEH:1:1106:22756:17724/1‑50 (MQ=60)
AATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTTTA > M01420:84:000000000‑ABVEH:1:1109:6693:6082/1‑50 (MQ=60)
ATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAAC < M01420:84:000000000‑ABVEH:1:1105:14673:9705/51‑1 (MQ=60)
ATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAAC < M01420:84:000000000‑ABVEH:1:2111:19753:27243/51‑1 (MQ=60)
AAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACGTCCAACC < M01420:84:000000000‑ABVEH:1:2114:22197:6113/51‑1 (MQ=60)
ATGTCAGTTGCCGGGGATTTTTTTTAACGTCCAACCGCCGCTTTAGGGCGT > M01420:84:000000000‑ABVEH:1:1101:6379:18255/1‑51 (MQ=60)
ATGTCAGTTGCCGGGGATTTTTTTTAACGTCCAACCGCCGCTTTAGGGCGT > M01420:84:000000000‑ABVEH:1:1103:9139:26421/1‑51 (MQ=60)
ATGTCAGTTGCCGGGGATTTTTTTTAACGTCCAACCGCCGCTTTAGGGCGT > M01420:84:000000000‑ABVEH:1:2104:13248:11852/1‑51 (MQ=60)
gtggccggggttTTTTTTTACCGTCCAACCGCCGCTTTAGGGCGTTTCTTC < M01420:84:000000000‑ABVEH:1:1113:17356:13477/39‑1 (MQ=60)
ggcgggggatTTTTTTTAACGTCCAACCGCCGCTTTAGGGCGTTTCTTCGC < M01420:84:000000000‑ABVEH:1:1110:20590:24480/41‑1 (MQ=60)
TTTTTTAAACGCCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATT < M01420:84:000000000‑ABVEH:1:1104:11352:6978/50‑1 (MQ=60)
TTTTTAACGTCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCA < M01420:84:000000000‑ABVEH:1:1109:23508:18231/50‑1 (MQ=60)
TTTAACGCCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACC < M01420:84:000000000‑ABVEH:1:1114:13901:5030/50‑1 (MQ=60)
TAACGCCCAGCCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACCGG < M01420:84:000000000‑ABVEH:1:2107:4053:19690/50‑1 (MQ=60)
AAACGCCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACCGG < M01420:84:000000000‑ABVEH:1:2103:20642:27784/50‑1 (MQ=60)
|
AGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTTAACGTCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACCGG > NC_017635/3375179‑3375277
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
