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
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,515,428 |
+C |
intergenic (+367/‑456) |
tRNA‑Pro (CGG) → / → pilB |
tRNA‑Pro/Type IV pilus assembly protein PilB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,515,427 | 1 | . | C | 94.7%
| 66.3
/ ‑2.9
| 19 | intergenic (+366/‑457) | tRNA‑Pro (CGG)/pilB | tRNA‑Pro/Type IV pilus assembly protein PilB |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (5/13); total (5/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑C‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCA > AM260479/3515299‑3515551
|
ggcggTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑ccttca < 2:1040755/134‑6 (MQ=255)
cggTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑Ttcatc < 2:699917/134‑1 (MQ=255)
ccGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGt < 1:525677/133‑1 (MQ=255)
ccGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGt < 2:1031839/133‑1 (MQ=255)
aGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCatgat < 2:627250/134‑1 (MQ=255)
gTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATgg < 2:412436/134‑1 (MQ=255)
ccAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGtctt < 1:37806/115‑1 (MQ=255)
ccAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGtctt > 2:37806/1‑115 (MQ=255)
cGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATcc < 1:513460/123‑1 (MQ=255)
cGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATcc > 2:513460/1‑123 (MQ=255)
gagaAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATcc < 1:500311/134‑1 (MQ=255)
cTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CATTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCg < 1:983885/133‑1 (MQ=255)
gCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATgg > 2:252472/1‑87 (MQ=255)
gCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATgg < 1:252472/87‑1 (MQ=255)
gCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGtcttc < 1:438208/69‑1 (MQ=255)
gCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGtcttc > 2:438208/1‑69 (MQ=255)
gCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTtga < 2:571333/134‑1 (MQ=255)
gATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGa < 2:287835/133‑1 (MQ=255)
tGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCa > 1:423009/1‑134 (MQ=255)
gCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGAGGAACTGCATGAAGGGCTTCCTGCAAATTGGCAt < 2:107997/131‑1 (MQ=255)
|
GGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑C‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCA > AM260479/3515299‑3515551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑C‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGC > AM260479/3515308‑3515564
|
gacaggcTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGG < GWNJ‑0478:712:GW2002102894th:2:1105:10399:63151/143‑1 (MQ=60)
atacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGT < GWNJ‑0478:712:GW2002102894th:2:1213:14462:41799/99‑1 (MQ=60)
TCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCC < GWNJ‑0478:712:GW2002102894th:2:2101:13172:17669/149‑1 (MQ=60)
cgtggggctcggagatgtgtataagagacagCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTC < GWNJ‑0478:712:GW2002102894th:2:1116:16390:63381/117‑1 (MQ=60)
CCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGctgtctcttatacacatctccgagcccacgagacggagc > GWNJ‑0478:712:GW2002102894th:2:2116:7815:67140/1‑111 (MQ=60)
CAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATC < GWNJ‑0478:712:GW2002102894th:2:1216:7469:40668/150‑1 (MQ=60)
TGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatg > GWNJ‑0478:712:GW2002102894th:2:1206:11379:52384/1‑98 (MQ=60)
CGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGC < GWNJ‑0478:712:GW2002102894th:2:1214:6337:70416/150‑1 (MQ=60)
CCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CATTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCT < GWNJ‑0478:712:GW2002102894th:2:2213:7124:93185/149‑1 (MQ=60)
CCTGCGCGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCAC > GWNJ‑0478:712:GW2002102894th:2:1210:7630:57615/1‑150 (MQ=60)
CGGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTG > GWNJ‑0478:712:GW2002102894th:2:2207:14287:38755/1‑150 (MQ=60)
GGGCATCTTGCTGACGGCC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGT < GWNJ‑0478:712:GW2002102894th:2:1103:13922:74897/150‑1 (MQ=60)
ataagagacagcC‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGC < GWNJ‑0478:712:GW2002102894th:2:2205:13846:69691/137‑1 (MQ=60)
|
ATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑C‑TTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGC > AM260479/3515308‑3515564
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
