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 |
AM260480 |
1,166,676 |
+G |
intergenic (+150/‑109) |
h16_B1032 → / → h16_B1033 |
conserved hypothetical protein/probable extra‑cytoplasmic solute receptor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 1,166,674 | 1 | . | G | 96.3%
| 95.7
/ ‑3.0
| 27 | intergenic (+148/‑111) | h16_B1032/h16_B1033 | conserved hypothetical protein/probable extra‑cytoplasmic solute receptor |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (14/12); total (14/13) |
| Fisher's exact test for biased strand distribution p-value = 4.81e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.08e-01 |
GGCCCGGCATCCCGGACCCAACATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCA‑GGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGA > AM260480/1166548‑1166791
|
ggCCCGGCATCCCGGACCCAACATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCA‑GGgtttt < 1:676871/134‑2 (MQ=255)
gCCCGGCATCCCGGACCCAACATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTc > 2:114195/1‑134 (MQ=255)
aaCATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATc < 2:776614/134‑1 (MQ=255)
tgATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGacaa > 2:924895/1‑133 (MQ=255)
aaGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACGTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGc > 2:646120/1‑134 (MQ=255)
ggTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGAcg > 1:321701/1‑134 (MQ=255)
ccGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTg < 2:321701/134‑1 (MQ=255)
ccGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGATCAAGCCGGTTGACGCGTg > 1:49526/1‑134 (MQ=255)
tttCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGcgcg > 1:622493/1‑83 (MQ=255)
tttCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGcgcg < 2:622493/83‑1 (MQ=255)
tttCGCCTTGCTGCCGTGGACCCCCCAGACCTAAATTCCCGTTTGCCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGCCAACAATTTGGCGTGATCGGTCAAGCCGTTTGACGCTGGGCGacc > 2:68692/1‑132 (MQ=255)
cTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGaa < 1:114195/134‑1 (MQ=255)
ccGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTgaga > 1:433832/1‑133 (MQ=255)
cGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGaaa < 1:646120/134‑1 (MQ=255)
cccAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCaa < 1:235859/134‑1 (MQ=255)
ccAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGATCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAAt < 2:49526/134‑1 (MQ=255)
gACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATc > 2:550459/1‑132 (MQ=255)
gACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATc > 1:896242/1‑132 (MQ=255)
gACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATc > 1:882737/1‑132 (MQ=255)
ccTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAaga < 2:896242/134‑1 (MQ=255)
gtgGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAg > 1:213531/1‑108 (MQ=255)
gtgGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAg < 2:213531/108‑1 (MQ=255)
ggCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAg > 1:980465/1‑133 (MQ=255)
gCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGa < 2:432592/134‑1 (MQ=255)
gCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGa < 1:924895/134‑1 (MQ=255)
cgAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGc > 2:254500/1‑46 (MQ=255)
cgAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGc < 1:254500/46‑1 (MQ=255)
|
GGCCCGGCATCCCGGACCCAACATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCA‑GGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGA > AM260480/1166548‑1166791
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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
GGAGGAACTGACGGCCCGGCATCCCGGACCCAACATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCA‑GGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGAAGCGAACCAATAACCTATGGTGGCGCGGATAC > AM260480/1166536‑1166823
|
cgtgggctcggagatgtgtataagagacagCAACATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCC < GWNJ‑0478:712:GW2002102894th:2:1105:16044:98419/119‑1 (MQ=60)
CGGCCCGGCATCCCGGACCCAACATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCG < GWNJ‑0478:712:GW2002102894th:2:2110:15451:66855/150‑1 (MQ=60)
tttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCC < GWNJ‑0478:712:GW2002102894th:2:1201:1910:15100/76‑1 (MQ=60)
ggagactttttctttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagaCA‑GGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACG < GWNJ‑0478:712:GW2002102894th:2:1205:14020:67789/64‑1 (MQ=60)
ACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGC > GWNJ‑0478:712:GW2002102894th:2:1204:1478:67711/1‑150 (MQ=60)
GCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGATCAAGCCGGTTGACGCGTGG > GWNJ‑0478:712:GW2002102894th:2:1102:5096:40337/1‑150 (MQ=60)
GTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTctgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:2108:4874:36342/1‑113 (MQ=60)
TCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAA > GWNJ‑0478:712:GW2002102894th:2:1213:14100:45890/1‑149 (MQ=60)
CCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGC < GWNJ‑0478:712:GW2002102894th:2:1108:20588:60204/150‑1 (MQ=60)
GCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCA > GWNJ‑0478:712:GW2002102894th:2:2208:10438:44866/1‑148 (MQ=60)
GCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCA > GWNJ‑0478:712:GW2002102894th:2:2207:13768:59602/1‑148 (MQ=60)
CCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGA < GWNJ‑0478:712:GW2002102894th:2:2109:18975:85090/150‑1 (MQ=60)
CCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGAC < GWNJ‑0478:712:GW2002102894th:2:1114:1859:90102/150‑1 (MQ=60)
GACCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGctgtctcttat > GWNJ‑0478:712:GW2002102894th:2:1115:15149:57882/1‑138 (MQ=60)
CCTCAATTGCCGTGTGGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGG > GWNJ‑0478:712:GW2002102894th:2:2214:5063:36228/1‑149 (MQ=60)
GGCCGATACCGCGAGCAGGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGAAGCGAACCAATAACC < GWNJ‑0478:712:GW2002102894th:2:2210:19807:16181/150‑1 (MQ=60)
ataagagacaggGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGAAGCGAACCAATAACCTATGGT < GWNJ‑0478:712:GW2002102894th:2:1208:14254:37687/138‑1 (MQ=60)
cagGGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGAAGCGAACCAATAACCTATGGTGGCGCGGAT < GWNJ‑0478:712:GW2002102894th:2:1104:12227:69793/147‑1 (MQ=60)
G‑GGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGAAGCGAACCAATAACCTATGGTGGCGCGGATAC > GWNJ‑0478:712:GW2002102894th:2:2101:19789:45939/1‑150 (MQ=60)
|
GGAGGAACTGACGGCCCGGCATCCCGGACCCAACATGTGATGGCGAAGGCGGGACCCGCGACGGTGTGGGTCCCGCTCTTTCGCCTTGCTGCCGTGGACCCCCCAGACCTCAATTGCCGTGTGGCCGATACCGCGAGCA‑GGTTTTCCCTCTGTTTGCGCGAATCGACAACAACTTGGCGTGATCGGTCAAGCCGGTTGACGCGTGGCGATCCGAGAATTGAGAAAAGACGGCAATCAAGAGGTACAGACATGAGGAAGCGAACCAATAACCTATGGTGGCGCGGATAC > AM260480/1166536‑1166823
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
