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 |
4,016,601 |
Δ1 bp |
coding (203/969 nt) |
h16_A3718 → |
probable extra‑cytoplasmic solute receptor,putative component of transport system, tripartite tricarboxylate transport (TTT) family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 4,016,601 | 0 | A | . | 100.0%
| 71.2
/ NA
| 17 | coding (203/969 nt) | h16_A3718 | probable extra‑cytoplasmic solute receptor,putative component of transport system, tripartite tricarboxylate transport (TTT) family |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (8/9); total (8/9) |
GCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACGACAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGA > AM260479/4016493‑4016696
|
gCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCa > 2:987102/1‑134 (MQ=255)
aTGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGAcc < 1:46220/134‑1 (MQ=255)
aTGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGAc < 1:987102/133‑1 (MQ=255)
cGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGtt > 2:908602/1‑134 (MQ=255)
gcggcTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAgg < 1:672611/134‑1 (MQ=255)
cggcTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAggg > 2:1028739/1‑134 (MQ=255)
gggCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACaa < 1:239406/104‑1 (MQ=255)
gggCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACaa > 2:239406/1‑104 (MQ=255)
ccgcGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATcgcg < 1:790306/73‑1 (MQ=255)
ccgcGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATcgcg > 2:790306/1‑73 (MQ=255)
cgATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGa < 1:1028739/134‑1 (MQ=255)
gatgatTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCt > 1:89299/1‑71 (MQ=255)
gatgatTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCt < 2:89299/71‑1 (MQ=255)
cgGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCAt < 1:875092/54‑1 (MQ=38)
cgGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCAt > 2:875092/1‑54 (MQ=38)
cgGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATAc > 2:211685/1‑78 (MQ=255)
cgGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATAc < 1:211685/78‑1 (MQ=255)
|
GCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACGACAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGA > AM260479/4016493‑4016696
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ 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
CACCTTCGCCGCCGCGCCGGCCTTTGCGCTCGATAGCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACGACAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCG > AM260479/4016458‑4016711
|
cgtgggctcggagatgtgtataagagacagCGATAGCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAA < GWNJ‑0478:712:GW2002102894th:2:1103:4944:65176/119‑1 (MQ=60)
caagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTT < GWNJ‑0478:712:GW2002102894th:2:2206:12011:50949/85‑1 (MQ=60)
gagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTC < GWNJ‑0478:712:GW2002102894th:2:2201:8311:87792/104‑1 (MQ=60)
ttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATAC < GWNJ‑0478:712:GW2002102894th:2:1207:4358:84713/71‑1 (MQ=60)
CATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACC < GWNJ‑0478:712:GW2002102894th:2:1102:15042:19218/150‑1 (MQ=60)
CATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATAC < GWNJ‑0478:712:GW2002102894th:2:2214:6792:11352/149‑1 (MQ=60)
gtagctccgtctcgtgggctcggagatgtgtataagagacaGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCC < GWNJ‑0478:712:GW2002102894th:2:1115:20026:37221/109‑1 (MQ=60)
aagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATG < GWNJ‑0478:712:GW2002102894th:2:1212:9583:98134/91‑1 (MQ=60)
gtgtataagagacagGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGC < GWNJ‑0478:712:GW2002102894th:2:1114:4209:88905/134‑1 (MQ=60)
GGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGC < GWNJ‑0478:712:GW2002102894th:2:2111:18254:97206/150‑1 (MQ=60)
CTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAActgtctcttatacacatctccgagcccacgagacggagctacatctcgt > GWNJ‑0478:712:GW2002102894th:2:1106:7448:10531/1‑101 (MQ=60)
gggctcggagatgtgtataagagacagGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGG < GWNJ‑0478:712:GW2002102894th:2:2103:14941:43491/122‑1 (MQ=60)
GCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCG < GWNJ‑0478:712:GW2002102894th:2:2216:21106:32968/150‑1 (MQ=60)
|
CACCTTCGCCGCCGCGCCGGCCTTTGCGCTCGATAGCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACGACAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCG > AM260479/4016458‑4016711
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
