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
|
150 |
26.0 |
2053212 |
90.0% |
1847890 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
1,464,435 |
T→C |
L40P (CTG→CCG) |
h16_A1354 → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,464,435 | 0 | T | C | 100.0%
| 90.4
/ NA
| 24 | L40P (CTG→CCG) | h16_A1354 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/14); total (10/14) |
GGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGC > AM260479/1464308‑1464558
|
ggAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcg > 2:781416‑M1/1‑132 (MQ=255)
tGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggc < 2:48122‑M1/134‑13 (MQ=255)
cGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcg < 2:779017‑M1/134‑17 (MQ=255)
tcatcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtac > 1:491925‑M1/1‑103 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGccgct < 1:586684/99‑1 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGccgct > 2:586684/1‑99 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccag < 2:146716‑M1/134‑34 (MQ=255)
atcaGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtac > 2:629468‑M1/1‑101 (MQ=255)
gCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagca < 2:808880‑M1/134‑38 (MQ=255)
cTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcac > 2:685341‑M1/1‑96 (MQ=255)
ggCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcatt < 1:629468‑M1/134‑45 (MQ=255)
gTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagc > 2:660099‑M1/1‑82 (MQ=255)
ccgccACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaata < 1:660099‑M1/133‑62 (MQ=255)
acacGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattggg > 2:239733‑M1/1‑67 (MQ=255)
acacGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattggg < 1:239733‑M1/114‑48 (MQ=255)
acacGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggc < 1:784227‑M1/85‑19 (MQ=255)
acacGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggc > 2:784227‑M1/1‑67 (MQ=255)
gAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaat < 1:685341‑M1/134‑72 (MQ=255)
gCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaatgggcccg < 2:491925‑M1/132‑79 (MQ=255)
gCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaatgggcccgcgccc > 2:440774‑M1/1‑51 (MQ=255)
ctctGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaatgggcccgcgcccgg < 2:131608‑M1/134‑86 (MQ=255)
tGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaatgggcccgcgcccggt < 1:781416‑M1/132‑87 (MQ=255)
gCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaatgggcccgcgcccggtcgac < 1:440774‑M1/134‑91 (MQ=255)
gCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaatgggcccgcgcccggtcgactggcctga > 1:561985‑M1/1‑36 (MQ=255)
ggTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaatgggcccgcgcccggtcgactggcctgataatgacggctgagcaggca < 2:561985‑M1/134‑119 (MQ=255)
ggTCGACAGCCGCTGGcgctgcacgggctgcggcgcctggatgtaccagagcacggcattgggtgagccgccgaatatgtggcgaatgggcccgcgcccggtcgactggcctgataatgacggctgagcaggca > 2:885858‑M1/1‑16 (MQ=255)
|
GGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGC > AM260479/1464308‑1464558
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ 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
TGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGCCCGGTCGACTGGCCTGAT > AM260479/1464303‑1464576
|
ggagatgtgtataagagacaGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCT < GWNJ‑0478:712:GW2002102894th:2:2107:11581:2949/130‑1 (MQ=60)
CGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACC > GWNJ‑0478:712:GW2002102894th:2:1214:10458:68008/1‑149 (MQ=60)
cgtctcgtgggctcggagatgtgtataagagacaggtccagcGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAG < GWNJ‑0478:712:GW2002102894th:2:2203:10377:25042/108‑1 (MQ=60)
CATCAGCTGGTGGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggt < GWNJ‑0478:712:GW2002102894th:2:2115:5808:101192/150‑10 (MQ=60)
GGGCGAACCGTCCAGC‑GTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggtgagccgccgaa < GWNJ‑0478:712:GW2002102894th:2:2108:11258:79792/150‑21 (MQ=60)
agacaggtccagcGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggtgagccgccgaatat < GWNJ‑0478:712:GW2002102894th:2:1116:5374:13141/137‑24 (MQ=60)
GCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGgcattgggtgagccgccgaatatgtggcgaatgggcc < GWNJ‑0478:712:GW2002102894th:2:2111:14823:66994/149‑38 (MQ=60)
CGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGCCCGGT < GWNJ‑0478:712:GW2002102894th:2:2113:4212:16850/150‑1 (MQ=60)
GCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGCCCGGTCGACTGGCCTGAT > GWNJ‑0478:712:GW2002102894th:2:2105:4016:38905/1‑150 (MQ=60)
GCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAGCCGCTGGCGCTGCACGGGCTGCGGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaagactagac > GWNJ‑0478:712:GW2002102894th:2:1201:17571:41967/1‑62 (MQ=60)
|
TGACAGGAGATGCCATGCACGCCTGTGACCTGTGTCATCAGCTGGTGGGCGAACCGTCCAGCAGTGCCGCCACACGAGCACCTGGCTGCCTCTGGCATTGCGGCCATGAGCAACCGGTGCAAGGTCGACAACTGCTGGTGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGCTGCACGGGCTGCGGCGCCTGGATGTACCAGAGCACGGCATTGGGTGAGCCGCCGAATATGTGGCGAATGGGCCCGCGCCCGGTCGACTGGCCTGAT > AM260479/1464303‑1464576
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
