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 |
1,089,440 |
Δ1 bp |
intergenic (+115/‑17) |
h16_A0996 → / → h16_A0997 |
FAD/FMN‑containing dehydrogenase/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,089,439 | 0 | C | . | 100.0%
| 101.2
/ NA
| 23 | intergenic (+114/‑18) | h16_A0996/h16_A0997 | FAD/FMN‑containing dehydrogenase/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (11/12); total (11/12) |
GGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGA > AM260479/1089316‑1089542
|
ggcggcGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag > 1:474923/1‑132 (MQ=255)
cgTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATccacagg > 2:680838/1‑119 (MQ=255)
cgTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATccacagg < 1:680838/122‑4 (MQ=255)
gCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGAc < 2:688484/134‑1 (MQ=255)
tAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCgg < 2:474923/134‑1 (MQ=255)
gACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCagag > 2:122448/1‑134 (MQ=255)
gcaggAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCgg > 1:961485/1‑118 (MQ=255)
gcaggAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCgg < 2:961485/118‑1 (MQ=255)
cAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCcac > 1:307495/1‑133 (MQ=255)
gCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag > 1:847726/1‑82 (MQ=255)
gCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag < 2:847726/82‑1 (MQ=255)
cGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAg < 1:338925/134‑1 (MQ=255)
gCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGc < 1:122448/133‑1 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATg < 2:400913/85‑1 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATg > 1:400913/1‑85 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGAc < 2:190339/89‑1 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGAc > 1:190339/1‑89 (MQ=255)
cccGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCg < 1:729313/86‑1 (MQ=255)
cccGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGCGAGAGCAGATCAGATGAGACCg > 2:729313/1‑86 (MQ=255)
cgcgGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAag < 2:1058942/134‑1 (MQ=255)
cAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGac < 1:956958/113‑1 (MQ=255)
cAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGac > 2:956958/1‑113 (MQ=255)
cATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGt > 1:680040/1‑97 (MQ=255)
cATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGt < 2:680040/97‑1 (MQ=255)
tGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAactggaactgga > 1:1031951/1‑134 (MQ=255)
|
GGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGA > AM260479/1089316‑1089542
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
GCCACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCCTTCGGCGATCCGGTGCAC > AM260479/1089294‑1089582
|
GCCACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGG < GWNJ‑0478:712:GW2002102894th:2:1105:15775:47443/150‑1 (MQ=60)
tttattttggtcagtttgttttttttttttcaagcagaagacggcatacgagcttagcgagtgtctcgtgggctcggagatgtgtataagagacaGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGC < GWNJ‑0478:712:GW2002102894th:2:2113:14108:87456/53‑1 (MQ=60)
CCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGC > GWNJ‑0478:712:GW2002102894th:2:1210:6471:78705/1‑148 (MQ=60)
CACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGA < GWNJ‑0478:712:GW2002102894th:2:1209:16234:37212/150‑1 (MQ=60)
gaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATC < GWNJ‑0478:712:GW2002102894th:2:1108:14917:7680/90‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATC < GWNJ‑0478:712:GW2002102894th:2:2212:18631:76588/120‑1 (MQ=60)
ATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGAT < GWNJ‑0478:712:GW2002102894th:2:2106:8592:5282/150‑1 (MQ=60)
gtctcgtgggctcggagatgtgtataagagacagGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTG < GWNJ‑0478:712:GW2002102894th:2:2109:16475:81874/116‑1 (MQ=60)
AATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGct > GWNJ‑0478:712:GW2002102894th:2:2209:3079:58229/1‑148 (MQ=60)
GGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACA > GWNJ‑0478:712:GW2002102894th:2:1203:17171:31227/1‑149 (MQ=60)
GGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCtgtctcttatacacatctccgagcccacgagacactc > GWNJ‑0478:712:GW2002102894th:2:2114:7097:90031/1‑113 (MQ=60)
GGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCActgtctcttatacacatctccgagcccacgagac > GWNJ‑0478:712:GW2002102894th:2:1206:6745:84852/1‑115 (MQ=60)
GGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTctgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:1113:12486:9096/1‑119 (MQ=60)
GCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTAC < GWNJ‑0478:712:GW2002102894th:2:1205:8030:25429/150‑1 (MQ=60)
GGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGA < GWNJ‑0478:712:GW2002102894th:2:1108:3720:40594/149‑1 (MQ=60)
gagacagGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAG < GWNJ‑0478:712:GW2002102894th:2:2209:10656:33894/143‑1 (MQ=60)
CGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACtgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:2107:9900:100114/1‑128 (MQ=60)
GCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGAC > GWNJ‑0478:712:GW2002102894th:2:2211:12970:52570/1‑150 (MQ=60)
agatgtgtataagagacagCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGTCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCATTCGGC < GWNJ‑0478:712:GW2002102894th:2:2212:21292:89321/131‑1 (MQ=60)
GTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaac > GWNJ‑0478:712:GW2002102894th:2:2204:10640:92697/1‑73 (MQ=60)
GTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGctgtctcttatacacatctccgagcccacgagacactc > GWNJ‑0478:712:GW2002102894th:2:2214:20115:24457/1‑112 (MQ=60)
GTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCCTTCGGCGATCCGGTGCAC > GWNJ‑0478:712:GW2002102894th:2:2206:11192:27102/1‑150 (MQ=60)
GTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCCTTCGGCGATCCGGTGCAC > GWNJ‑0478:712:GW2002102894th:2:2108:19195:42730/1‑150 (MQ=60)
|
GCCACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCCTTCGGCGATCCGGTGCAC > AM260479/1089294‑1089582
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
