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
|
146 |
27.9 |
2327082 |
89.7% |
2087392 |
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%
| 90.8
/ NA
| 21 | 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 . (11/10); total (11/10) |
GGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG > AM260479/3515185‑3515427
|
ggCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCcg > 1:769186/1‑134 (MQ=255)
ggAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGt < 1:431685/134‑1 (MQ=255)
ggAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGt < 1:967725/134‑1 (MQ=255)
aaaCAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGc > 1:623304/1‑134 (MQ=255)
gACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCg < 2:836865/134‑1 (MQ=255)
cccACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTg < 2:623304/134‑1 (MQ=255)
cATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTcc < 1:828359/134‑1 (MQ=255)
gggCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGt > 2:688281/1‑134 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACt > 1:306017/1‑107 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACt < 2:306017/107‑1 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGaa < 1:1134045/121‑1 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGaa > 2:1134045/1‑121 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTcc > 1:294273/1‑125 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTcc < 2:294273/125‑1 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCtt > 1:1156766/1‑133 (MQ=255)
aaGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGaaa > 2:682477/1‑132 (MQ=255)
aaGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGaaa < 1:682477/132‑1 (MQ=255)
cTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACgg > 2:453606/1‑134 (MQ=255)
cTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACgg > 2:71791/1‑134 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACt < 1:902255/98‑1 (MQ=255)
cgcgGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACt > 2:902255/1‑98 (MQ=255)
|
GGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG > AM260479/3515185‑3515427
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
TGAATGCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGT > AM260479/3515169‑3515457
|
TGAATGCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTC < GWNJ‑0478:712:GW2002102894th:2:1209:11065:75751/148‑1 (MQ=60)
GAATGCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGC > GWNJ‑0478:712:GW2002102894th:2:2110:4606:94171/1‑150 (MQ=60)
GAATGCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCG < GWNJ‑0478:712:GW2002102894th:2:2202:17869:76040/149‑1 (MQ=60)
GCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAG < GWNJ‑0478:712:GW2002102894th:2:1214:11284:80309/149‑1 (MQ=60)
CAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCC > GWNJ‑0478:712:GW2002102894th:2:2102:9913:60506/1‑150 (MQ=60)
CGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCT < GWNJ‑0478:712:GW2002102894th:2:1209:17240:54382/150‑1 (MQ=60)
CGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCT < GWNJ‑0478:712:GW2002102894th:2:2209:9307:91916/150‑1 (MQ=60)
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGctgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:1203:17409:22135/1‑137 (MQ=60)
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTG > GWNJ‑0478:712:GW2002102894th:2:1201:11889:48786/1‑149 (MQ=60)
CTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTG > GWNJ‑0478:712:GW2002102894th:2:2216:13540:68467/1‑149 (MQ=60)
ACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAA < GWNJ‑0478:712:GW2002102894th:2:2215:8743:63705/149‑1 (MQ=60)
GCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCC < GWNJ‑0478:712:GW2002102894th:2:2115:3205:93478/150‑1 (MQ=60)
CGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCC < GWNJ‑0478:712:GW2002102894th:2:2106:3515:14973/150‑1 (MQ=60)
cggagatgtgtataagagacAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCG < GWNJ‑0478:712:GW2002102894th:2:2202:8527:4824/130‑1 (MQ=60)
ATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATGGT > GWNJ‑0478:712:GW2002102894th:2:1103:7051:95937/1‑150 (MQ=60)
|
TGAATGCCTCCAGGTCGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATGGT > AM260479/3515169‑3515457
|
| 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: ‑ |
