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 |
582,589 |
T→G |
H295Q (CAT→CAG) |
h16_A0555 → |
zinc metalloprotease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 582,589 | 0 | T | G | 96.7%
| 106.2
/ ‑3.7
| 30 | H295Q (CAT→CAG) | h16_A0555 | zinc metalloprotease |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base G (14/15); minor base A (0/1); total (14/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.57e-01 |
GCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCATGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGC > AM260479/582473‑582701
|
gCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATttctt < 1:317369/134‑1 (MQ=255)
gggcAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCt > 2:832264/1‑134 (MQ=255)
gggcAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCt > 2:395674/1‑134 (MQ=255)
ggcAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTg < 1:395674/134‑1 (MQ=255)
cAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAAGGCATGCCCGATTCCTTCATGCGGCTGCa < 1:991608/134‑1 (MQ=255)
gCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATc > 1:206762/1‑134 (MQ=255)
gCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATc > 2:482480/1‑134 (MQ=255)
tCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCGTGCCCGATTTCTTCATGCg > 1:802790/1‑101 (MQ=255)
tCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCg < 2:802790/101‑1 (MQ=255)
ggCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATttc > 1:231977/1‑79 (MQ=255)
ggCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATttc < 2:231977/79‑1 (MQ=255)
gAGCGCGAGTCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCg > 2:237673/1‑134 (MQ=255)
cgAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACt > 1:541442/1‑133 (MQ=255)
ggTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCg < 2:1005959/100‑1 (MQ=255)
ggTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCg > 1:1005959/1‑100 (MQ=255)
gCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCa > 1:50380/1‑67 (MQ=255)
gCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCa < 2:50380/67‑1 (MQ=255)
cTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGc > 2:473462/1‑134 (MQ=255)
cAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGa < 2:240315/133‑1 (MQ=255)
aGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGAtt < 2:534259/134‑1 (MQ=255)
aGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGAtt < 2:541442/134‑1 (MQ=255)
aGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGAtt < 2:206762/134‑1 (MQ=255)
aGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGAtt < 1:473462/134‑1 (MQ=255)
ccGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGAtt < 2:253008/125‑1 (MQ=255)
ccGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGAtt > 1:253008/1‑125 (MQ=255)
cgcgGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGc < 1:832264/134‑1 (MQ=255)
cggcggGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGaa > 1:881054/1‑71 (MQ=255)
cggcggGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGaa < 2:881054/71‑1 (MQ=255)
ggTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGAc > 1:584942/1‑91 (MQ=255)
ggTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGAc < 2:584942/91‑1 (MQ=255)
|
GCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCATGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGC > AM260479/582473‑582701
|
| 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
ACGCGCAGCCCGGACGCCGCGGCGGCGCTGGCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCATGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCGTCAGCCATGCCAGCAAGCGCA > AM260479/582443‑582731
|
cgatgtggatcgcgctggcctcgatggtgctggcgggcctgcccgcccatGGCCAGCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGC < GWNJ‑0478:712:GW2002102894th:2:2115:8089:41622/100‑1 (MQ=60)
gacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCC < GWNJ‑0478:712:GW2002102894th:2:2210:11092:63206/93‑1 (MQ=60)
AGCCCGGACGCCGCGGCGGCGCTGGCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCC < GWNJ‑0478:712:GW2002102894th:2:1111:14628:39194/150‑1 (MQ=60)
CGCCGCGGCGGCGCTGGCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTT < GWNJ‑0478:712:GW2002102894th:2:1216:14038:71973/150‑1 (MQ=60)
GGCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCG < GWNJ‑0478:712:GW2002102894th:2:1204:6587:27990/150‑1 (MQ=60)
GGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCG > GWNJ‑0478:712:GW2002102894th:2:1115:9145:17401/1‑150 (MQ=60)
GGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGG < GWNJ‑0478:712:GW2002102894th:2:1211:20116:17515/150‑1 (MQ=60)
GCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAAGGCATGCCCGATTCCTTCATGCGGCTGCAGCGCGCATCGGGGAC < GWNJ‑0478:712:GW2002102894th:2:2214:13791:64577/150‑1 (MQ=60)
ATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCGTGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCctgtctcttatacacatct > GWNJ‑0478:712:GW2002102894th:2:2202:2199:6894/1‑131 (MQ=60)
ttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCC < GWNJ‑0478:712:GW2002102894th:2:1111:4107:27672/76‑1 (MQ=60)
GTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCtgtctcttatacacatctccgagcccacgagacggagct > GWNJ‑0478:712:GW2002102894th:2:1114:10494:59572/1‑110 (MQ=60)
GCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTC > GWNJ‑0478:712:GW2002102894th:2:2103:13161:61116/1‑149 (MQ=60)
gagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACC < GWNJ‑0478:712:GW2002102894th:2:2208:1454:96917/104‑1 (MQ=60)
GCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCtgtctcttatacacatctc > GWNJ‑0478:712:GW2002102894th:2:2215:12427:42935/1‑131 (MQ=60)
AGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgc > GWNJ‑0478:712:GW2002102894th:2:1102:17843:48790/1‑98 (MQ=60)
GCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGC > GWNJ‑0478:712:GW2002102894th:2:1116:3844:84612/1‑150 (MQ=60)
TCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTctgtctcttatacacatctccgagcccacgagacggagctacatctcgt > GWNJ‑0478:712:GW2002102894th:2:2207:8810:16264/1‑101 (MQ=60)
gggctcggagatgtgtataagagacagCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGAC < GWNJ‑0478:712:GW2002102894th:2:1210:16029:59772/123‑1 (MQ=60)
CAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGAC < GWNJ‑0478:712:GW2002102894th:2:1215:20917:51909/150‑1 (MQ=60)
TCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCtgtctcttatacacatctccgagcccac > GWNJ‑0478:712:GW2002102894th:2:2104:7992:69743/1‑122 (MQ=60)
CCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCGTCAGCC < GWNJ‑0478:712:GW2002102894th:2:2205:20178:5935/150‑1 (MQ=60)
GGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCtgtctcttatacacatct > GWNJ‑0478:712:GW2002102894th:2:1107:18219:99473/1‑132 (MQ=60)
CCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2201:15206:25895/1‑77 (MQ=60)
|
ACGCGCAGCCCGGACGCCGCGGCGGCGCTGGCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCATGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCGTCAGCCATGCCAGCAAGCGCA > AM260479/582443‑582731
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
