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
|
150 |
26.0 |
2053212 |
90.0% |
1847890 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,515,314 |
Δ1 bp |
intergenic (+253/‑570) |
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 | 3,515,314 | 0 | G | . | 100.0%
| 99.9
/ NA
| 23 | intergenic (+253/‑570) | tRNA‑Pro (CGG)/pilB | tRNA‑Pro/Type IV pilus assembly protein PilB |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (16/7); total (16/7) |
GCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCT > AM260479/3515186‑3515440
|
gCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGTACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCcgc < 2:723188/134‑1 (MQ=255)
gcgGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAg > 2:67496/1‑134 (MQ=255)
cGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTc > 1:736990/1‑134 (MQ=255)
cGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTc > 1:795033/1‑134 (MQ=255)
tGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTc > 2:93995/1‑134 (MQ=255)
gggCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGt > 2:186702/1‑134 (MQ=255)
cgcgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCt > 2:302136/1‑134 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCtt > 1:1023389/1‑133 (MQ=255)
gCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGaaa < 2:666619/134‑1 (MQ=255)
gCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGa > 2:997211/1‑132 (MQ=255)
gCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGa > 2:183305/1‑132 (MQ=255)
gTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACt > 2:111156/1‑97 (MQ=255)
gTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACt < 1:111156/97‑1 (MQ=255)
gTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCt > 1:411266/1‑134 (MQ=255)
gTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTACTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCt > 1:794258/1‑134 (MQ=255)
gCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGAt > 1:31862/1‑134 (MQ=255)
gccgccTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACt > 2:345219/1‑106 (MQ=255)
gccgccTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACt < 1:345219/106‑1 (MQ=255)
gccTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGAc < 1:648828/134‑1 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑cct > 1:346213/1‑132 (MQ=255)
gcggcgGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑cctt < 1:997211/134‑4 (MQ=255)
gcggcgGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑cctt < 1:183305/134‑4 (MQ=255)
aaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtct > 1:429169/1‑134 (MQ=255)
|
GCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCT > AM260479/3515186‑3515440
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
CTTGAATGCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGC > AM260479/3515167‑3515445
|
CTTGAATGCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTC > GWNJ‑0478:712:GW2002102894th:2:2110:4438:5734/1‑150 (MQ=60)
GAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCG > GWNJ‑0478:712:GW2002102894th:2:2114:17407:22405/1‑150 (MQ=60)
GAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCG > GWNJ‑0478:712:GW2002102894th:2:2203:21005:96281/1‑150 (MQ=60)
cggagatgtgtataagagacaGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAG < GWNJ‑0478:712:GW2002102894th:2:1108:20615:41576/128‑1 (MQ=60)
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTG > GWNJ‑0478:712:GW2002102894th:2:2216:6993:81429/1‑149 (MQ=60)
GGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTC > GWNJ‑0478:712:GW2002102894th:2:1210:4008:18089/1‑150 (MQ=60)
GGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTACTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTC > GWNJ‑0478:712:GW2002102894th:2:2203:21126:91457/1‑150 (MQ=60)
AGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATG > GWNJ‑0478:712:GW2002102894th:2:1105:13810:20296/1‑150 (MQ=60)
gtataagagacagACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCG < GWNJ‑0478:712:GW2002102894th:2:1206:20615:17931/136‑1 (MQ=60)
GTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑Cctt > GWNJ‑0478:712:GW2002102894th:2:1206:7969:24482/1‑147 (MQ=60)
CGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTC < GWNJ‑0478:712:GW2002102894th:2:2109:8419:100914/150‑1 (MQ=60)
CCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTT > GWNJ‑0478:712:GW2002102894th:2:1213:2359:20948/1‑150 (MQ=60)
CGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGC < GWNJ‑0478:712:GW2002102894th:2:1113:15596:80484/150‑1 (MQ=60)
CGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGC < GWNJ‑0478:712:GW2002102894th:2:2215:3110:30835/150‑1 (MQ=60)
|
CTTGAATGCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGC > AM260479/3515167‑3515445
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
