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
|
149 |
26.7 |
2337422 |
87.5% |
2045244 |
105.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
782,333 |
+A |
intergenic (‑683/‑39) |
h16_A0723 ← / → h16_A0724 |
hypothetical membrane protein/hypothetical membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 782,333 | 1 | . | A | 95.8%
| 82.0
/ ‑3.6
| 24 | intergenic (‑683/‑39) | h16_A0723/h16_A0724 | hypothetical membrane protein/hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (13/10); total (14/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGTACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGC‑A‑TG‑GCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATC > AM260479/782217‑782449
|
tGTACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATTA‑GCCTGGACCATAGcc > 2:1102306/1‑134 (MQ=255)
tACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCg < 1:1102306/134‑1 (MQ=255)
ggCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCg > 2:469452/1‑124 (MQ=255)
ggCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCg < 1:469452/124‑1 (MQ=255)
gcgcCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGcc > 2:287586/1‑134 (MQ=255)
aGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCa > 1:854379/1‑134 (MQ=255)
aGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCa > 1:75943/1‑134 (MQ=255)
tACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCAtt < 1:1142254/134‑1 (MQ=255)
tGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGAc > 1:103158/1‑134 (MQ=255)
tCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTg > 2:553911/1‑133 (MQ=255)
gccgcTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAg > 2:100038/1‑134 (MQ=255)
cgcTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCg > 2:495249/1‑134 (MQ=255)
cgcTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCg < 2:75943/134‑1 (MQ=255)
cgcTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCg < 2:854379/134‑1 (MQ=255)
ggCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGc > 1:514274/1‑126 (MQ=255)
ggCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGc < 2:514274/126‑1 (MQ=255)
ggCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGt < 1:100038/134‑1 (MQ=255)
gcgcTGCCACAGAATATCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGa > 2:40107/1‑134 (MQ=255)
tCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCtt < 1:40107/134‑1 (MQ=255)
tCAGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCt < 1:495249/133‑1 (MQ=255)
aGGGGGATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGa > 1:1079315/1‑134 (MQ=255)
ggggATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATc > 2:1054151/1‑134 (MQ=255)
gggATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGc > 1:559718/1‑44 (MQ=255)
gggATGGGGAGCGA‑TGAGCCTGGACCATAGCCCGGCAGCAACGc < 2:559718/44‑1 (MQ=25)
|
TGTACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGC‑A‑TG‑GCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATC > AM260479/782217‑782449
|
| 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
CCCGCGCAGGCCTTGGTTCTGCTTGTACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGC‑ATG‑GCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATCGTGGCATGGGCATTCAAAACGAGGGGCTTCACC > AM260479/782194‑782482
|
ccgttctgtgcgtctgttttgttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGAC < GWNJ‑0478:712:GW2002102894th:2:2210:12319:56394/59‑1 (MQ=60)
GCAGGCCTTGGTTCTGCTTGTACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAG < GWNJ‑0478:712:GW2002102894th:2:2208:1498:33713/150‑1 (MQ=60)
GTACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGG < GWNJ‑0478:712:GW2002102894th:2:2214:1461:5568/150‑1 (MQ=60)
GTACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGG < GWNJ‑0478:712:GW2002102894th:2:1210:18948:95737/150‑1 (MQ=60)
CGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCtgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:2211:13228:69319/1‑120 (MQ=60)
GACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCAT > GWNJ‑0478:712:GW2002102894th:2:1104:1799:83317/1‑150 (MQ=60)
GACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCAT > GWNJ‑0478:712:GW2002102894th:2:2116:12077:29567/1‑150 (MQ=60)
GAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACC > GWNJ‑0478:712:GW2002102894th:2:1106:1989:43271/1‑150 (MQ=60)
GTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGC < GWNJ‑0478:712:GW2002102894th:2:2215:13081:85671/150‑1 (MQ=60)
gtctcgtggctcggagatgtgtataagagacagGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCC < GWNJ‑0478:712:GW2002102894th:2:1116:19314:41164/116‑1 (MQ=60)
GCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTG > GWNJ‑0478:712:GW2002102894th:2:1215:13134:19381/1‑150 (MQ=60)
AGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGG < GWNJ‑0478:712:GW2002102894th:2:1106:17022:24485/150‑1 (MQ=60)
gtctcgtgggctcggagatgtgtataagagacaG‑GCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATC < GWNJ‑0478:712:GW2002102894th:2:2203:18910:32468/117‑1 (MQ=60)
CTGCCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGAT > GWNJ‑0478:712:GW2002102894th:2:2212:1945:95374/1‑150 (MQ=60)
CCACAGAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGTGGTCAGTGATGTCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1216:11169:29924/1‑75 (MQ=60)
GAATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGctgtctcttatacacat > GWNJ‑0478:712:GW2002102894th:2:1107:18686:25917/1‑133 (MQ=60)
ATATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCtgtctcttatacacatctccgagcccacgagacactcgctaaactcgtatgccgtcttc > GWNJ‑0478:712:GW2002102894th:2:2112:19171:63061/1‑91 (MQ=60)
TATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaa > GWNJ‑0478:712:GW2002102894th:2:2208:2199:42150/1‑79 (MQ=60)
ATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATCGTGGCATGGGC < GWNJ‑0478:712:GW2002102894th:2:1105:6898:56379/150‑1 (MQ=60)
ATCAGGGGGATGGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATCGTGGCATGGG < GWNJ‑0478:712:GW2002102894th:2:1212:1971:24782/149‑1 (MQ=60)
GGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATCGTGGCATGGGCATTCAAAACG < GWNJ‑0478:712:GW2002102894th:2:1216:4374:3179/149‑1 (MQ=60)
GGGGAGCGATGAGCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATCGTGGCATGGGCATTCAAAACG < GWNJ‑0478:712:GW2002102894th:2:1201:13836:22509/149‑1 (MQ=60)
A‑GCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGActgtctcttatacacatctccgagcccacgagacactcgctaagctcgtatgccgtcttctgcttgaaaaaaaaaacaattgaaactgtacgtcatgagaaccatagggg > GWNJ‑0478:712:GW2002102894th:2:1214:20079:48887/1‑40 (MQ=60)
|
CCCGCGCAGGCCTTGGTTCTGCTTGTACATCGGTGGGCGCCTGACCAGAATGGAGCCAGTACATCGATGCATCGCCGCTGCATTGCCAAGAAGAAATCAGGCCGGCGCTGCCACAGAATATCAGGGGGATGGGGAGC‑ATG‑GCCTGGACCATAGCCCGGCAGCAACGCCGGGGTCAGTGATGTCGCGGCATTGGCTGGACCTGGAGCGTCTCCGGGCCTACAGCGTTGCCGTGCTGATCATCTATGGTGCCTTGATCGTGGCATGGGCATTCAAAACGAGGGGCTTCACC > AM260479/782194‑782482
|
| 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: ‑ |
