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 |
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%
| 54.2
/ NA
| 13 | 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 . (4/9); total (4/9) |
AAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACGACAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCGAGACCAACAAGCCGC > AM260479/4016498‑4016726
|
aaGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGAGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATcgcg < 2:672478/134‑1 (MQ=255)
aTGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGAc < 1:1012979/133‑1 (MQ=255)
cGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGtt > 2:376333/1‑134 (MQ=255)
aaCCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCaa > 1:429605/1‑133 (MQ=255)
cggcggcTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACaa < 1:347391/134‑1 (MQ=255)
cggcggcTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACaa < 1:408180/134‑1 (MQ=255)
gcggcTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGAc < 1:320470/111‑1 (MQ=255)
gcggcTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGAc > 2:320470/1‑111 (MQ=255)
tGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAAcc < 1:124394/133‑1 (MQ=255)
cAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAAt < 2:429605/134‑1 (MQ=255)
ggCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTg < 1:376333/134‑1 (MQ=255)
aaGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCGAGACcaa > 2:270356/1‑133 (MQ=255)
cTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACAGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCGAGACCAACAAgccgc < 1:442568/134‑1 (MQ=255)
|
AAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACGACAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCGAGACCAACAAGCCGC > AM260479/4016498‑4016726
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
CCTTCGCCGCCGCGCCGGCCTTTGCGCTCGATAGCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACGACAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCGAGACCAACAAGCCGCCGGTCACGCTGAAGAACGCCACCC > AM260479/4016460‑4016750
|
CCTTCGCCGCCGCGCCGGCCTTTGCGCTCGATAGCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGG < GWNJ‑0478:712:GW2002102894th:2:2102:18438:49613/150‑1 (MQ=60)
GTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAAT > GWNJ‑0478:712:GW2002102894th:2:1213:2871:12381/1‑149 (MQ=60)
aagagacaGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATAC < GWNJ‑0478:712:GW2002102894th:2:1204:16225:48866/142‑1 (MQ=60)
CATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATAC < GWNJ‑0478:712:GW2002102894th:2:2215:20973:81452/149‑1 (MQ=60)
GCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGC < GWNJ‑0478:712:GW2002102894th:2:1206:9162:22152/150‑1 (MQ=60)
GCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGC < GWNJ‑0478:712:GW2002102894th:2:1211:5372:87756/150‑1 (MQ=60)
TTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGG < GWNJ‑0478:712:GW2002102894th:2:1109:13625:31858/149‑1 (MQ=60)
CGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCG < GWNJ‑0478:712:GW2002102894th:2:1208:16366:101097/150‑1 (MQ=60)
GCTTCATACG‑CAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACAGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCGAGACCAACAAGCCGCCGGTCACGCTGAAGA < GWNJ‑0478:712:GW2002102894th:2:1213:2951:82755/150‑1 (MQ=60)
GCAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCGAGACCAACAAGCCGCCGGTCACGCTGAAGAACGCCACCC < GWNJ‑0478:712:GW2002102894th:2:1107:6928:13671/150‑1 (MQ=60)
|
CCTTCGCCGCCGCGCCGGCCTTTGCGCTCGATAGCGTCAAGGTCATGATCGGCGCCAACCCCGGCGGCGGCTTTGACCAGACCGGCCGCTCGCTGGGCGCCGCGATGATTGCCGCGGGCCAGGCCAAGACCGCTTCATACGACAACAAGGGCGGCGCCGGCGGCACCATCGCGCTGACCCAGTTCGTCAATACCGACAAGGGCAACCCCAATGCGCTGATGGTGGTGGGCGCGGTGATGGTGGGCGCGATCGAGACCAACAAGCCGCCGGTCACGCTGAAGAACGCCACCC > AM260479/4016460‑4016750
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
