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
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260480 |
1,537,213 |
G→A |
G347D (GGC→GAC) |
h16_B1373 → |
Acyl‑CoA synthetase (AMP‑forming)/AMP‑acid ligase II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 1,537,213 | 0 | G | A | 96.4%
| 100.6
/ ‑5.2
| 28 | G347D (GGC→GAC) | h16_B1373 | Acyl‑CoA synthetase (AMP‑forming)/AMP‑acid ligase II |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (13/14); total (13/15) |
| 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 |
CCATGGCTACGGCATGACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGGCAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAGCGCCGAGGCCCTGCGGCCCGA > AM260480/1537088‑1537321
|
ccATGGCTACGGCATGACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCgg > 2:72668/1‑134 (MQ=255)
aTGACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGc > 2:118747/1‑133 (MQ=255)
aCCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAAcc < 1:979360/134‑1 (MQ=255)
cGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTa < 1:733804/134‑1 (MQ=255)
ttCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAgg < 1:549531/132‑1 (MQ=255)
tGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGccc > 1:1029277/1‑134 (MQ=255)
cGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGt > 1:948669/1‑134 (MQ=255)
gCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTg < 2:57906/134‑1 (MQ=255)
ggACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATgc > 2:547149/1‑134 (MQ=255)
ccGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGcgcg < 1:779851/134‑1 (MQ=255)
cGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCgg < 1:118747/134‑1 (MQ=255)
cgcACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCTGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAAccc < 1:11832/90‑1 (MQ=255)
cgcACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCTGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAAccc > 2:11832/1‑90 (MQ=255)
cgcACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTg < 1:768281/75‑1 (MQ=255)
cgcACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTg > 2:768281/1‑75 (MQ=255)
cgcACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTg > 2:763632/1‑75 (MQ=255)
cgcACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTg < 1:763632/75‑1 (MQ=255)
cgcACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTa > 1:539415/1‑99 (MQ=255)
cgcACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTa < 2:539415/99‑1 (MQ=255)
cTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTg > 2:268035/1‑109 (MQ=255)
cTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTg < 1:268035/109‑1 (MQ=255)
ggcgggcgAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGGCAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCatcacgc < 1:563248/133‑7 (MQ=255)
gcgAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAgc > 1:363129/1‑134 (MQ=255)
gagCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTg > 2:251740/1‑81 (MQ=255)
gagCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTg < 1:251740/81‑1 (MQ=255)
gagCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAGCGCCGAGGCCCTGCGGCCCGa < 1:72668/134‑1 (MQ=255)
tAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAAcc < 2:753889/40‑1 (MQ=38)
tAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAAcc > 1:753889/1‑40 (MQ=38)
ggaggaCAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTg > 2:220/1‑61 (MQ=255)
ggaggaCAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTg < 1:220/61‑1 (MQ=255)
|
CCATGGCTACGGCATGACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGGCAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAGCGCCGAGGCCCTGCGGCCCGA > AM260480/1537088‑1537321
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ 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
GCGATGTTCGGCCAGCCGCTGCACCATGGCTACGGCATGACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGGCAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAGCGCCGAGGCCCTGCGGCCCGACGGCTGGCTCAATACCGGCGACATCGGCCG > AM260480/1537065‑1537351
|
GCGATGTTCGGCCAGCCGCTGCACCATGGCTACGGCATGACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGAC < GWNJ‑0478:712:GW2002102894th:2:1106:10256:97097/150‑1 (MQ=60)
CCGCTGCACCATGGCTACGGCATGACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCtgtc > GWNJ‑0478:712:GW2002102894th:2:1206:5931:58544/1‑146 (MQ=60)
gatgtagctccgtctcgtgggctcgtagatgtgtataagagacagCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCC < GWNJ‑0478:712:GW2002102894th:2:2116:10412:42611/105‑1 (MQ=60)
gatgtagctccgtctcgtgggctcggagatgtgtataagagacagCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCC < GWNJ‑0478:712:GW2002102894th:2:2116:9549:15644/105‑1 (MQ=60)
GACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGAT < GWNJ‑0478:712:GW2002102894th:2:2213:11524:68373/150‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCTGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATC < GWNJ‑0478:712:GW2002102894th:2:1101:3022:87185/120‑1 (MQ=60)
GCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCC < GWNJ‑0478:712:GW2002102894th:2:2115:18933:50162/150‑1 (MQ=60)
CGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCG > GWNJ‑0478:712:GW2002102894th:2:2216:8688:35694/1‑150 (MQ=60)
TCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTG > GWNJ‑0478:712:GW2002102894th:2:2210:15909:96636/1‑150 (MQ=60)
GTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATG < GWNJ‑0478:712:GW2002102894th:2:2103:12627:87333/148‑1 (MQ=60)
gctccgtctcgtgggctcggagatgtgtataagagacAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTAC < GWNJ‑0478:712:GW2002102894th:2:1116:8468:58855/113‑1 (MQ=60)
ataagagacaGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTAC < GWNJ‑0478:712:GW2002102894th:2:1201:10877:71775/140‑1 (MQ=60)
aagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTAC < GWNJ‑0478:712:GW2002102894th:2:1101:18144:3300/91‑1 (MQ=60)
CGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCctgtctcttatacacatctcc > GWNJ‑0478:712:GW2002102894th:2:2103:12845:17557/1‑129 (MQ=60)
ACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCAC < GWNJ‑0478:712:GW2002102894th:2:2201:21005:12911/150‑1 (MQ=60)
CCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTAATACCGCGCACC < GWNJ‑0478:712:GW2002102894th:2:1108:8879:97976/150‑1 (MQ=60)
CCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAGCG > GWNJ‑0478:712:GW2002102894th:2:1208:12717:6304/1‑150 (MQ=60)
CGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGGCAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCAtcacgccgggccccctgatcc < GWNJ‑0478:712:GW2002102894th:2:2102:11685:92534/149‑22 (MQ=60)
GTGCAGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2114:20265:60215/1‑71 (MQ=60)
AGAGCTGCGGGTAGTCGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAGCGCCGAGGCCCTGCGGCCCGACGGCTGGCTCAATAC < GWNJ‑0478:712:GW2002102894th:2:1107:16778:4406/150‑1 (MQ=60)
CGGGCCGGAGGACAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAGCGCCGAGGCCCTGCGGCCCGACGGCTGGCTCAATACCGGCGACATCGGCCG > GWNJ‑0478:712:GW2002102894th:2:1215:10419:21079/1‑150 (MQ=60)
|
GCGATGTTCGGCCAGCCGCTGCACCATGGCTACGGCATGACCGAATATGCGGGGTCGCTGTTCGTGACCCGCATGGACCGGCCGCGCACCGATTGCTCGGCGGGCGAGATCGTCGAAGGTGCAGAGCTGCGGGTAGTCGGGCCGGAGGGCAAGCCGGTGCCGCAGGGGCAACCCGGCGAGCTATGGATCAGGGGGCCCGGCGTGATGCGCGGCTACTACCGCGCACCGGACCTGAGCGCCGAGGCCCTGCGGCCCGACGGCTGGCTCAATACCGGCGACATCGGCCG > AM260480/1537065‑1537351
|
| 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: ‑ |
