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 |
1,056,947 |
+G |
intergenic (+211/‑15) |
h16_A0964 → / → h16_A0965 |
conserved hypothetical protein/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,056,945 | 1 | . | G | 95.2%
| 71.9
/ ‑2.8
| 21 | intergenic (+209/‑17) | h16_A0964/h16_A0965 | conserved hypothetical protein/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (10/10); total (10/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01 |
TTAGCTTCTGTTGCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCA‑GGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGCCAGGGCCGGGTTGAGCGGCTGGTGCCGCTG > AM260479/1056813‑1057063
|
ttAGCTTCTGTTGCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCA‑g > 2:148218/1‑134 (MQ=255)
gCTTCTGTTGCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCA‑gggc < 2:974035/134‑3 (MQ=255)
gCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGccgcccgc > 2:367217/1‑132 (MQ=255)
tgctgcACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAgg > 1:29640/1‑134 (MQ=255)
cacaAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGc < 1:367217/132‑1 (MQ=255)
cacaAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGc < 1:576812/132‑1 (MQ=255)
cAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGc > 1:144650/1‑123 (MQ=255)
cAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGc < 2:144650/123‑1 (MQ=255)
gccgGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCAc > 2:870959/1‑132 (MQ=255)
gccgGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCAc > 2:428583/1‑132 (MQ=255)
gCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACcgc < 1:428583/134‑1 (MQ=255)
tggCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGAcccc < 1:870959/134‑1 (MQ=255)
gCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCA‑‑‑‑‑‑‑‑‑‑CCTGC‑‑‑TGGCGGGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGaa < 2:508234/134‑1 (MQ=255)
gTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGaa < 1:401206/131‑1 (MQ=255)
gTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGaa > 2:401206/1‑131 (MQ=255)
cAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCcagca < 2:626825/62‑1 (MQ=255)
cAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCcagca > 1:626825/1‑62 (MQ=255)
aGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGcc < 2:29640/134‑1 (MQ=255)
ccGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGt < 2:359092/84‑1 (MQ=255)
ccGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGt > 1:359092/1‑84 (MQ=255)
ggCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACTTCGAcc < 2:644692/72‑1 (MQ=255)
ggCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGAcc > 1:644692/1‑72 (MQ=255)
ggCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGCCAGGGCCGGGTTGAGCGGCTGGTGCCGCTg > 1:34095/1‑134 (MQ=255)
|
TTAGCTTCTGTTGCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCA‑GGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGCCAGGGCCGGGTTGAGCGGCTGGTGCCGCTG > AM260479/1056813‑1057063
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCATTAGCTTCTGTTGCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCA‑GGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGCCAGGGCCGGGTTGAGCGGCTGGTGCCGCTGCGCTACGGCCGCATGATCCAGTCGCC > AM260479/1056810‑1057089
|
GCATTAGCTTCTGTTGCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCA‑GGgcctcgacagt > GWNJ‑0478:712:GW2002102894th:2:1207:5822:79589/1‑138 (MQ=60)
gttttttttttggtttttttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGC < GWNJ‑0478:712:GW2002102894th:2:2109:5799:70156/50‑1 (MQ=60)
AGCTTCTGTTGCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGT > GWNJ‑0478:712:GW2002102894th:2:1105:5891:9342/1‑150 (MQ=60)
ATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGC > GWNJ‑0478:712:GW2002102894th:2:1111:2416:54318/1‑150 (MQ=60)
GCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACG < GWNJ‑0478:712:GW2002102894th:2:1208:13279:46684/148‑1 (MQ=60)
GCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACG < GWNJ‑0478:712:GW2002102894th:2:2104:13439:14578/148‑1 (MQ=60)
GGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTG < GWNJ‑0478:712:GW2002102894th:2:1213:5909:6509/150‑1 (MQ=60)
GTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAA < GWNJ‑0478:712:GW2002102894th:2:2206:20787:51520/150‑1 (MQ=60)
ACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGC < GWNJ‑0478:712:GW2002102894th:2:1211:9316:48634/150‑1 (MQ=60)
CGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtct > GWNJ‑0478:712:GW2002102894th:2:2108:17936:43425/1‑92 (MQ=60)
TCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCtgtctcttatacacatctccgagcccacnagnnnnnn > GWNJ‑0478:712:GW2002102894th:2:1209:12256:101301/1‑112 (MQ=60)
GGGTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCtgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:1206:12414:95701/1‑115 (MQ=60)
GTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACctgtctcttatacacatctccgagcccacgcgacggagctacatctcg > GWNJ‑0478:712:GW2002102894th:2:2109:18024:55143/1‑102 (MQ=60)
GTACTGTCGAGGCCCGGCGCGAGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGCCAGGGCCGGGTTGAGCGGCTGGTGCCGCTGC > GWNJ‑0478:712:GW2002102894th:2:1105:4382:38094/1‑150 (MQ=60)
cgtgcgcaccGCGCGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGCCAGGGCCGGGTTGAGCGGCTGGTGCCGCTGCGCTACGGCCGC > GWNJ‑0478:712:GW2002102894th:2:2114:16467:15843/11‑149 (MQ=60)
CGGCAGGGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGCCAGGGCCGGGTTGAGCGGCTGGTGCCGCTGCGCTACGGCCGCATGATCCAGTCGCC > GWNJ‑0478:712:GW2002102894th:2:2114:17320:52195/1‑150 (MQ=60)
|
GCATTAGCTTCTGTTGCAGATGCTGCACAAATGGCAACCGCCGGCGGCGCCGGCATTGGGGGCATGGTGGCGACACGTCAGGAGGGCGGGCAAGCCGTGGCCAAGGGTACTGTCGAGGCCCGGCGCGAGCGCGGCA‑GGCCGCCCGCCAGCAGGTGCCGCGCGGTGCGCACGAGGCCATCGGCAACGTCGACCGCGACCCCGTCGAACTGCTGGAAATCAGCAGCCAGGGCCGGGTTGAGCGGCTGGTGCCGCTGCGCTACGGCCGCATGATCCAGTCGCC > AM260479/1056810‑1057089
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
