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 |
AM260480 |
2,018,102 |
+C |
intergenic (+111/+98) |
h16_B1778 → / ← h16_B1779 |
putative peptidase/putative peptidase, S33 family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 2,018,101 | 1 | . | C | 100.0%
| 110.4
/ NA
| 29 | intergenic (+110/+99) | h16_B1778/h16_B1779 | putative peptidase/putative peptidase, S33 family |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (12/17); total (12/17) |
CGTTCAGGTCGTTGCGCTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGA‑CATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCGAGCAC > AM260480/2017972‑2018223
|
cGTTCAGGTCGTTGCGCTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGA‑ccat < 2:725558/134‑4 (MQ=255)
aGGTCGTTGCGCTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATgcgc < 2:32237/133‑1 (MQ=255)
cTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCTGGGGCATGCCCGACCATGCGCACCGATGGCCAg > 1:877208/1‑134 (MQ=255)
cTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAg > 1:832304/1‑134 (MQ=255)
aGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCACGCGCACCGATGGCCAgcgc < 1:631440/134‑1 (MQ=255)
cgcgGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGcgccg < 1:440581/134‑1 (MQ=255)
gCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCgccgcc > 2:689451/1‑132 (MQ=255)
cAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCATTGGCTACAGGCCCCGAGCCGCCATGGCTTGGCGCCCGCTTATCCGGGCGCATGGTCCGGGGCAGGCCCGACCATGCGCACCAATGGCCAGCGCCGCCCAg < 2:628307/134‑1 (MQ=255)
gggcgCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAgcgc < 2:1030397/134‑1 (MQ=255)
cTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAg > 1:467887/1‑133 (MQ=255)
cTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGt < 2:312993/134‑1 (MQ=255)
ttCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAgcgc < 2:46281/89‑1 (MQ=255)
ttCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAgcgc > 1:46281/1‑89 (MQ=255)
cAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTAt < 1:660098/133‑1 (MQ=255)
aGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTg < 2:687527/134‑1 (MQ=255)
gccgccCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTc > 1:252369/1‑109 (MQ=255)
gccgccCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTc < 2:252369/109‑1 (MQ=255)
cGTGCCCGCTTATCCGGGCGCATGGTCTGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGccc < 2:877208/132‑1 (MQ=255)
cGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGccc < 2:832304/132‑1 (MQ=255)
cGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCg > 2:131217/1‑134 (MQ=255)
cGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCg > 2:242894/1‑134 (MQ=255)
cGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCg > 1:36429/1‑134 (MQ=255)
cTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTc < 2:467887/134‑1 (MQ=255)
tCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTg > 2:627109/1‑76 (MQ=255)
tCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTg < 1:627109/76‑1 (MQ=255)
aTGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGAt < 2:136269/57‑1 (MQ=38)
aTGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGAt > 1:136269/1‑57 (MQ=38)
ccGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAgcgc < 1:1029821/121‑1 (MQ=255)
ccGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAgcgc > 2:1029821/1‑121 (MQ=255)
ggCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCGAGCAc < 1:131217/134‑1 (MQ=255)
|
CGTTCAGGTCGTTGCGCTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGA‑CATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCGAGCAC > AM260480/2017972‑2018223
|
| 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
GTTCAGGTCGTTGCGCTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGA‑CATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCGAGCACCGCCTGCGCAAACGCCGTGGGCGCTTC > AM260480/2017973‑2018250
|
GTTCAGGTCGTTGCGCTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCTGGGGCATGCCCGACCATGCGCACCGATGGCCAGC > GWNJ‑0478:712:GW2002102894th:2:2206:16874:91529/1‑150 (MQ=60)
GTTCAGGTCGTTGCGCTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGC > GWNJ‑0478:712:GW2002102894th:2:2205:2469:6363/1‑150 (MQ=60)
agcgggcacgaagcaagggcggctCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCG > GWNJ‑0478:712:GW2002102894th:2:2113:14599:9142/25‑149 (MQ=60)
GAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCACGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATG < GWNJ‑0478:712:GW2002102894th:2:2108:16976:71519/150‑1 (MQ=60)
GCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCC < GWNJ‑0478:712:GW2002102894th:2:1213:9905:72040/150‑1 (MQ=60)
attcagtttcttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGC < GWNJ‑0478:712:GW2002102894th:2:1107:2217:98202/63‑1 (MQ=60)
atgtagctccgtctcgtgggctcggagatgtgtataagagacaGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAG < GWNJ‑0478:712:GW2002102894th:2:2108:20519:45184/107‑1 (MQ=60)
GAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGT > GWNJ‑0478:712:GW2002102894th:2:1215:14793:23313/1‑149 (MQ=60)
AAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCtgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:1102:6981:18858/1‑120 (MQ=60)
GCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCctgtctcttat > GWNJ‑0478:712:GW2002102894th:2:1116:5151:80139/1‑139 (MQ=60)
TCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCAT < GWNJ‑0478:712:GW2002102894th:2:2111:8578:47301/149‑1 (MQ=60)
CCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGT > GWNJ‑0478:712:GW2002102894th:2:1105:5575:53656/1‑150 (MQ=60)
CGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCctgtctcttatacacatctccgaacccacgagacggagctacatctcgtatgccgtcttctgc > GWNJ‑0478:712:GW2002102894th:2:1111:15982:4047/1‑87 (MQ=60)
CCGGGCGCATGGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCGAGC < GWNJ‑0478:712:GW2002102894th:2:2216:15453:73986/149‑1 (MQ=60)
GGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtctt > GWNJ‑0478:712:GW2002102894th:2:1106:9712:11576/1‑91 (MQ=60)
GGTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCtgtctcttatacacatctccgagcccacgagacggagctac > GWNJ‑0478:712:GW2002102894th:2:2105:19436:32118/1‑109 (MQ=60)
GTCCGGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCtgtctcttatacacatctccgagcccacgagacggagctacat > GWNJ‑0478:712:GW2002102894th:2:2206:15035:20845/1‑107 (MQ=60)
gtcGGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCGAGCACCGCCTGCGCAA > GWNJ‑0478:712:GW2002102894th:2:2110:14019:55346/4‑149 (MQ=60)
GGGCATGCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCGAGCACCGCCTGCGCAAACGC < GWNJ‑0478:712:GW2002102894th:2:1109:4288:73566/150‑1 (MQ=60)
tgccccggacCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCtgtctcttatacacatctccgagc > GWNJ‑0478:712:GW2002102894th:2:1210:18666:72794/11‑126 (MQ=60)
GCCCGACCATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCtgtctcttatacacatcccgagcccac > GWNJ‑0478:712:GW2002102894th:2:1211:6840:42645/1‑123 (MQ=60)
C‑CATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCtgtctcttatacacatctccgagcccacgagac > GWNJ‑0478:712:GW2002102894th:2:2206:17494:98441/1‑117 (MQ=60)
|
GTTCAGGTCGTTGCGCTGAGCGCGGCAGGCGGGCGGCGGCGGGCGCTGAAGCATGGCAATGCCTTCAGCGCCCGAGCCGCCCTTGCTTCGTGCCCGCTTATCCGGGCGCATGGTCCGGGGCATGCCCGA‑CATGCGCACCGATGGCCAGCGCCGCCCAGCTCCGATGCCAGCGCTGACAGCGTCATGGCAGCCAGTATCAGCAATCTGCGCATTGCGCCCCTCATGCGTCAGCGCCTGTCTACATCGAGCACCGCCTGCGCAAACGCCGTGGGCGCTTC > AM260480/2017973‑2018250
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
