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 |
1,464,365 |
Δ1 bp |
coding (49/552 nt) |
h16_A1354 → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,464,365 | 0 | A | . | 100.0%
| 120.5
/ NA
| 27 | coding (49/552 nt) | h16_A1354 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (14/13); total (14/13) |
GCGGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCAC > AM260479/1464250‑1464478
|
gcgGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCAcc < 1:48197/134‑1 (MQ=255)
cagcaCAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTgg < 2:132833/134‑1 (MQ=255)
caATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTg > 2:705434/1‑134 (MQ=255)
caATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTg > 1:566912/1‑134 (MQ=255)
aTGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCg > 1:662563/1‑134 (MQ=255)
gggCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAg > 1:231543/1‑134 (MQ=255)
gggCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAg < 2:662563/134‑1 (MQ=255)
gccgcGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCgg < 2:231543/134‑1 (MQ=255)
cgcgCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTg > 2:901836/1‑134 (MQ=255)
atcatcGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGt > 1:390557/1‑134 (MQ=255)
cATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgg < 2:390557‑M1/134‑11 (MQ=255)
cATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgg < 2:304309‑M1/134‑11 (MQ=255)
tgACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcct > 2:957442‑M1/1‑112 (MQ=255)
cTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggat > 1:89234‑M1/1‑108 (MQ=255)
tcatcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAg < 2:263013/75‑1 (MQ=255)
tcatcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAg > 1:263013/1‑75 (MQ=255)
tcatcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCgg < 2:244828/82‑1 (MQ=255)
tcatcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCgg > 1:244828/1‑82 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCg < 2:503048/65‑1 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCg > 1:503048/1‑65 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccag < 1:957442‑M1/134‑34 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccag < 1:901836‑M1/134‑34 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtacca < 2:89234‑M1/133‑33 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtac > 1:838934‑M1/1‑101 (MQ=255)
cTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcac > 1:113229‑M1/1‑96 (MQ=255)
gCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGTCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggct < 2:986947‑M1/102‑14 (MQ=255)
gCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGTCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggct > 1:986947‑M1/1‑89 (MQ=255)
|
GCGGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCAC > AM260479/1464250‑1464478
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
CGCGGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGC > AM260479/1464249‑1464497
|
CGCGGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCA < GWNJ‑0478:712:GW2002102894th:2:1102:4894:32890/150‑1 (MQ=60)
ttttttcttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCA < GWNJ‑0478:712:GW2002102894th:2:2108:15888:61549/63‑1 (MQ=60)
GCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGC > GWNJ‑0478:712:GW2002102894th:2:2105:2875:46192/1‑150 (MQ=60)
AATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGG > GWNJ‑0478:712:GW2002102894th:2:2111:16345:61369/1‑150 (MQ=60)
GTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCtgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:2208:2459:12887/1‑121 (MQ=60)
CAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGC > GWNJ‑0478:712:GW2002102894th:2:1114:5879:57482/1‑150 (MQ=60)
GGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTC > GWNJ‑0478:712:GW2002102894th:2:1209:19875:88466/1‑150 (MQ=60)
gagatgtgtataagagacaGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTG < GWNJ‑0478:712:GW2002102894th:2:2101:7469:63797/131‑1 (MQ=60)
ATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATG > GWNJ‑0478:712:GW2002102894th:2:1106:1634:8122/1‑150 (MQ=60)
CGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCtgtctcttatacacatctccgagcccacgagacggagctacatc > GWNJ‑0478:712:GW2002102894th:2:1201:13247:54986/1‑106 (MQ=60)
CGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAgcctgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:1116:7429:33552/1‑110 (MQ=60)
CCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccg > GWNJ‑0478:712:GW2002102894th:2:1216:5866:10724/1‑95 (MQ=60)
CCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACC > GWNJ‑0478:712:GW2002102894th:2:2205:18402:48831/1‑147 (MQ=60)
GACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACG > GWNJ‑0478:712:GW2002102894th:2:1108:7005:61705/1‑150 (MQ=60)
GTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGTCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTctgtctcttatacacatc > GWNJ‑0478:712:GW2002102894th:2:2214:3563:38645/1‑132 (MQ=60)
CATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggt < GWNJ‑0478:712:GW2002102894th:2:2208:11971:45971/150‑10 (MQ=60)
CATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggt < GWNJ‑0478:712:GW2002102894th:2:2212:11302:74673/150‑10 (MQ=60)
GTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTctgtctcttatacacatctccgagcccacgagacggagctacat > GWNJ‑0478:712:GW2002102894th:2:1109:14344:50570/1‑106 (MQ=60)
|
CGCGGCAATGGGTGCAGCACAATGGCTGAGGGCGCCGCCGCGCAATCATCGCCGTGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGC > AM260479/1464249‑1464497
|
| 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: ‑ |
