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
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
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 | 100.0%
| 103.7
/ NA
| 27 | intergenic (+366/‑457) | tRNA‑Pro (CGG)/pilB | tRNA‑Pro/Type IV pilus assembly protein PilB |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (11/16); total (11/16) |
GGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCAT > AM260479/3515302‑3515549
|
ggTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTtcat > 2:857222/1‑132 (MQ=255)
aaaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGt < 1:748043/133‑1 (MQ=255)
aaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtct > 1:621606/1‑134 (MQ=255)
cttCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtcttc < 1:180635/129‑1 (MQ=255)
cgcgAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCa > 1:648191/1‑134 (MQ=255)
gAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCatga > 1:49502/1‑134 (MQ=255)
aGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCt < 1:628315/134‑1 (MQ=255)
gACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCtt < 2:49502/134‑1 (MQ=255)
cGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCtt > 1:288223/1‑134 (MQ=255)
gTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCtt > 1:155958/1‑133 (MQ=255)
tGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCa < 1:648997/134‑1 (MQ=255)
ccTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCt < 2:288223/134‑1 (MQ=255)
cGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCAACCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTgcg > 1:283652/1‑134 (MQ=255)
gCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCgg < 2:942146/74‑1 (MQ=255)
gCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCgg > 1:942146/1‑74 (MQ=255)
gCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTgcgc > 1:889353/1‑134 (MQ=255)
gCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTgc < 2:155958/132‑1 (MQ=255)
gCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTgc < 1:460765/132‑1 (MQ=255)
cccACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTtg < 2:118961/128‑1 (MQ=255)
cccACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTtg > 1:118961/1‑128 (MQ=255)
ggCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTtg < 2:785699/134‑1 (MQ=255)
gATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGa < 2:738473/133‑1 (MQ=255)
cgcgGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGc < 1:857222/133‑1 (MQ=255)
tGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAAtt > 2:196711/1‑127 (MQ=255)
tGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAAtt < 1:196711/127‑1 (MQ=255)
gCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCAt < 2:621606/131‑1 (MQ=255)
gCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCAt < 2:648191/131‑1 (MQ=255)
|
GGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCAT > AM260479/3515302‑3515549
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGCACGCACTTTTGAT > AM260479/3515290‑3515577
|
CGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTC < GWNJ‑0478:712:GW2002102894th:2:1204:1531:74015/150‑1 (MQ=60)
CCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTT > GWNJ‑0478:712:GW2002102894th:2:2108:19417:10690/1‑150 (MQ=60)
GGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCAT > GWNJ‑0478:712:GW2002102894th:2:2109:3495:77182/1‑150 (MQ=60)
GAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGAT > GWNJ‑0478:712:GW2002102894th:2:1102:21040:42971/1‑150 (MQ=60)
GAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGA < GWNJ‑0478:712:GW2002102894th:2:2114:18840:54498/149‑1 (MQ=60)
gcTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGT < GWNJ‑0478:712:GW2002102894th:2:1113:9207:65086/144‑1 (MQ=60)
GGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTC > GWNJ‑0478:712:GW2002102894th:2:1202:7195:35179/1‑150 (MQ=60)
GCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTC > GWNJ‑0478:712:GW2002102894th:2:1110:4894:20245/1‑149 (MQ=60)
AAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCT < GWNJ‑0478:712:GW2002102894th:2:2108:19348:52461/150‑1 (MQ=60)
GTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGG < GWNJ‑0478:712:GW2002102894th:2:2109:19510:81868/150‑1 (MQ=60)
tttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGC < GWNJ‑0478:712:GW2002102894th:2:2102:9775:100326/79‑1 (MQ=60)
CCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCAACCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGC > GWNJ‑0478:712:GW2002102894th:2:1202:16786:2332/1‑150 (MQ=60)
CTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCC > GWNJ‑0478:712:GW2002102894th:2:2207:2176:67140/1‑150 (MQ=60)
CTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTGTCTCTtatacacatctccgagcccacgagacggagctacatct > GWNJ‑0478:712:GW2002102894th:2:2210:18722:86327/1‑112 (MQ=60)
TTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCT > GWNJ‑0478:712:GW2002102894th:2:1108:6102:97870/1‑150 (MQ=60)
atgtagctccgtctcgtgggctcggagatgtgtataagagacagTCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAAC < GWNJ‑0478:712:GW2002102894th:2:2106:2924:50359/106‑1 (MQ=60)
CGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAAC < GWNJ‑0478:712:GW2002102894th:2:1212:19309:85579/148‑1 (MQ=60)
GCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGC < GWNJ‑0478:712:GW2002102894th:2:2209:8752:65209/149‑1 (MQ=60)
GGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGT < GWNJ‑0478:712:GW2002102894th:2:1112:13256:59280/150‑1 (MQ=60)
GGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctg > GWNJ‑0478:712:GW2002102894th:2:2214:11576:37276/1‑90 (MQ=60)
GGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctg > GWNJ‑0478:712:GW2002102894th:2:1103:18739:42845/1‑90 (MQ=60)
ATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATG > GWNJ‑0478:712:GW2002102894th:2:1205:18734:58668/1‑150 (MQ=60)
CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGCctgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:2113:18396:17195/1‑137 (MQ=60)
|
CGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGTCATCCCTTTCTCTCTTCATCCTCGATCGCCAGGTGCAGCGGCTTGTGCGCCTTCTTGATGAACTGCATGAAGGGCTTCCTGCAAATTGGCATCACGCAGTGTTATGCACGCACTTTTGAT > AM260479/3515290‑3515577
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
