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 |
3,375,228 |
(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 | 88.5%
| 77.9
/ 4.6
| 26 | intergenic (+36/+6) | yqhH/ygiQ | lipoprotein YqhH/YgiQ family radical SAM protein |
| Reads supporting (aligned to +/- strand): ref base . (0/3); new base T (12/11); total (12/14) |
| Fisher's exact test for biased strand distribution p-value = 2.25e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGTACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCA > NC_017635/3375172‑3375266
|
tGTACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGa > 1:578168/1‑50 (MQ=255)
gTACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑t > 2:1402388/1‑50 (MQ=255)
gTACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑t > 1:2055004/1‑50 (MQ=255)
tACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑t < 1:475843/49‑1 (MQ=255)
aCGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑ttt > 1:2028293/1‑50 (MQ=255)
cAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑tttttt < 2:1443062/50‑1 (MQ=255)
gAATGATAAAAAAATCCACGGCAGCATGTCAGTTGCCGGGGA‑tttttttt < 1:1818319/50‑2 (MQ=255)
aTAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑t < 2:246241/50‑1 (MQ=37)
aaaaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑Tcc < 1:100755/49‑1 (MQ=37)
aaaaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑Tcc < 2:1629769/49‑1 (MQ=37)
aaaaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑Tcc > 1:1680680/1‑49 (MQ=37)
aaaaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCa < 2:946360/50‑1 (MQ=37)
aaaaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCa < 2:1993238/50‑1 (MQ=37)
aaaaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCa < 1:289166/50‑1 (MQ=37)
aaaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCaa > 1:767666/1‑50 (MQ=38)
aaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAAc < 1:882495/50‑1 (MQ=38)
aaaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAAc < 1:1784232/50‑1 (MQ=38)
aaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAAcc < 1:1557758/50‑1 (MQ=38)
aaaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAAcc > 2:1506704/1‑50 (MQ=38)
aaTCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAAccg < 1:1456408/50‑1 (MQ=38)
ccGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCt > 2:719340/1‑50 (MQ=38)
ccGGCAGCATGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCt > 2:1068751/1‑50 (MQ=38)
gcaTGTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCTTTAggg > 1:1028607/1‑50 (MQ=39)
gTCAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGtt > 2:7156/1‑50 (MQ=39)
tCAGTTGCCGGGGA‑TTTTTTTAAACG‑TCCAACCGCCGCTTTAGGGCGttt < 2:619392/50‑1 (MQ=38)
cAGTTGCCGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGTttc > 2:991230/1‑50 (MQ=39)
aGTTGCCGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGTttct > 2:213406/1‑50 (MQ=39)
aGTTGCCGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGTttct > 1:100283/1‑50 (MQ=39)
gTTGCCGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGTttctt > 1:1973158/1‑50 (MQ=39)
ttGCGGGGGT‑TTTTTTTAAACG‑CCCAACCGCCGCTTTAGGGCGTttcttc < 2:1003250/50‑1 (MQ=255)
cGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCAc < 1:775569/50‑1 (MQ=255)
cGGGGATTTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCAc > 1:1027574/1‑50 (MQ=255)
gggT‑TTTTTTT‑AAGGCTCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCa < 1:138285/50‑1 (MQ=255)
|
TGTACGCAGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTT‑AACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCA > NC_017635/3375172‑3375266
|
| 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‑TTTTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACCG > NC_017635/3375179‑3375276
|
AGAATGATAAAAAAATCCACGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTTT < M01420:85:000000000‑AC936:1:2111:9690:16856/51‑1 (MQ=60)
AATGATAAAAAAATCCCTGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTTtaa < M01420:85:000000000‑AC936:1:2105:11542:27436/51‑4 (MQ=60)
AAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCCA < M01420:85:000000000‑AC936:1:1104:25427:24585/51‑1 (MQ=60)
AAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCC < M01420:85:000000000‑AC936:1:1102:25218:12190/50‑1 (MQ=60)
AAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCCA > M01420:85:000000000‑AC936:1:2109:23639:20796/1‑50 (MQ=60)
AAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCCAAC < M01420:85:000000000‑AC936:1:2111:17216:6381/51‑1 (MQ=60)
AAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCCAAC > M01420:85:000000000‑AC936:1:1111:6293:12919/1‑51 (MQ=60)
AAAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCCAAC < M01420:85:000000000‑AC936:1:1112:10130:26741/51‑1 (MQ=60)
AAAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCCAACC < M01420:85:000000000‑AC936:1:2108:14013:5800/51‑1 (MQ=60)
AAATCCCCGGCAGCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCCAACCG < M01420:85:000000000‑AC936:1:2106:19617:20424/51‑1 (MQ=60)
GCATGTCAGTTGCCGGGGATTTTTTTTAACG‑TCCAACCGCCGCTTTAGGGC > M01420:85:000000000‑AC936:1:1114:23075:25848/1‑51 (MQ=60)
AGTTGCCGGGGATTTTTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTT > M01420:85:000000000‑AC936:1:1102:18571:12032/1‑51 (MQ=60)
GTTGCCGGGGATTTTTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTC > M01420:85:000000000‑AC936:1:2113:17415:17393/1‑51 (MQ=60)
CCGGGGATTTTTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCAC < M01420:85:000000000‑AC936:1:1111:16907:15318/51‑1 (MQ=60)
CGGGGATTTTTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACC > M01420:85:000000000‑AC936:1:1114:14786:25386/1‑51 (MQ=60)
GGGGT‑TTTTTTTAAGGCTCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCA < M01420:85:000000000‑AC936:1:1102:6209:23724/51‑1 (MQ=40)
GGGATTTTTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAG < M01420:85:000000000‑AC936:1:1103:15492:16493/51‑1 (MQ=60)
atTTTTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCAT > M01420:85:000000000‑AC936:1:1111:26652:19593/3‑51 (MQ=60)
TTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCA < M01420:85:000000000‑AC936:1:2104:4221:21733/50‑1 (MQ=60)
TTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACCG > M01420:85:000000000‑AC936:1:2110:10714:17823/1‑51 (MQ=60)
TTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACC < M01420:85:000000000‑AC936:1:1111:15889:6461/50‑1 (MQ=60)
TTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACC < M01420:85:000000000‑AC936:1:1104:20465:12966/50‑1 (MQ=60)
TTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACC < M01420:85:000000000‑AC936:1:1102:6475:14949/50‑1 (MQ=60)
TTTAACA‑TCCATCCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACC < M01420:85:000000000‑AC936:1:1114:24357:17163/50‑1 (MQ=60)
|
AGAATGATAAAAAAATCCCCGGCAGCATGTCAGTTGCCGGGGA‑TTTTTTTAACG‑TCCAACCGCCGCTTTAGGGCGTTTCTTCGCACCAGCATTCACCG > NC_017635/3375179‑3375276
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
