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
|
155 |
25.8 |
2285122 |
88.0% |
2010907 |
104.3 |
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%
| 91.9
/ 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 . (10/11); total (10/11) |
GGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCT > AM260479/3515191‑3515440
|
ggAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGt < 1:963793/134‑1 (MQ=255)
gCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTc > 1:1030448/1‑134 (MQ=255)
gggCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCcg > 2:775933/1‑95 (MQ=255)
gggCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCcg < 1:775933/95‑1 (MQ=255)
gcgcGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTcc > 2:186190/1‑134 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAg < 1:1086533/122‑1 (MQ=255)
cgAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAg > 2:1086533/1‑122 (MQ=255)
aGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGt > 2:996746/1‑121 (MQ=255)
aGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGt < 1:996746/121‑1 (MQ=255)
aGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGa > 2:390423/1‑133 (MQ=255)
gTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCt > 2:21156/1‑134 (MQ=255)
ccgGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGt < 2:133187/71‑1 (MQ=255)
ccgGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGt > 1:133187/1‑71 (MQ=255)
gTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTAGCCCACCGGCGTGAAAAACtt < 2:95001/134‑1 (MQ=255)
aTTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATgcg < 1:186190/134‑1 (MQ=255)
aaaCTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTcc < 2:1030448/134‑1 (MQ=255)
tATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCAACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCAt > 2:12309/1‑134 (MQ=255)
ggCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTg < 1:390423/133‑1 (MQ=255)
ggcggTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑ccttca < 2:837569/134‑6 (MQ=255)
aaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtct > 1:75911/1‑134 (MQ=255)
aaTCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGtct < 1:21156/134‑1 (MQ=255)
|
GGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCT > AM260479/3515191‑3515440
|
| 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
CGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATG > AM260479/3515184‑3515455
|
gctcggagatgtgtataagagacaGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGA < GWNJ‑0478:712:GW2002102894th:2:2113:4230:95187/126‑1 (MQ=60)
CGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCT < GWNJ‑0478:712:GW2002102894th:2:2206:20420:65359/150‑1 (MQ=60)
CTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCC > GWNJ‑0478:712:GW2002102894th:2:2210:6104:40584/1‑150 (MQ=60)
ACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAA < GWNJ‑0478:712:GW2002102894th:2:2214:17018:28747/150‑1 (MQ=60)
GCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAG < GWNJ‑0478:712:GW2002102894th:2:2208:16659:56812/148‑1 (MQ=60)
GTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgt > GWNJ‑0478:712:GW2002102894th:2:1109:13279:12545/1‑102 (MQ=60)
AATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCAT < GWNJ‑0478:712:GW2002102894th:2:1110:18061:99832/150‑1 (MQ=60)
CGGCCGCCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATC < GWNJ‑0478:712:GW2002102894th:2:1206:10710:58805/149‑1 (MQ=60)
CCTCCGCGGCGGTGAAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTT > GWNJ‑0478:712:GW2002102894th:2:1104:15002:78882/1‑150 (MQ=60)
AAATCTGC‑TTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGGCCTTCATCAGGTCTTCTGCGGTCATGATG < GWNJ‑0478:712:GW2002102894th:2:1103:16952:38125/150‑1 (MQ=60)
|
CGGCCGCGGAAAACAGCTGGCTACGACCCACTACTGCATGGGGCGCGAGCTTGCCGTCGCGCACCAGCCGCCGGAAGGTGGCAATTGAAACTTCGAGGTATTCGGCCGCCTCCGCGGCGGTGAAATCTGCGTTCCGCGAGGTGGCCAAAGACTTCCTCGTGCGAGAAGTCCTCGTCCTTGAAAGCCTGCTCGCCCACCGGCGTGAAAAACTTGATGCGCTCCTGCGCGGGCATCTTGCTGACGG‑CTTCATCAGGTCTTCTGCGGTCATGATG > AM260479/3515184‑3515455
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
