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 |
AM260479 |
2,594,128 |
Δ1 bp |
coding (326/957 nt) |
cR ← |
Recombinational DNA repair protein (RecF pathway) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 2,594,128 | 0 | C | . | 100.0%
| 86.4
/ NA
| 20 | coding (326/957 nt) | cR | Recombinational DNA repair protein (RecF pathway) |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (10/10); total (10/10) |
TCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCTTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGCGCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCCAGCAGGTC > AM260479/2593999‑2594252
|
tCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGc < 2:127510/134‑1 (MQ=255)
tgcAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAg > 1:909006/1‑134 (MQ=255)
cagGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCgg < 2:711535/134‑1 (MQ=255)
cTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGccc > 1:246378/1‑132 (MQ=255)
cTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGccc > 1:736993/1‑132 (MQ=255)
cTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGccc > 2:16850/1‑132 (MQ=255)
cTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCT‑CAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAg > 1:799097/1‑134 (MQ=255)
cGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCtttt < 1:16850/134‑1 (MQ=255)
agcaCCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATc < 2:826747/113‑1 (MQ=255)
agcaCCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATc > 1:826747/1‑113 (MQ=255)
cTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCt < 2:736993/134‑1 (MQ=255)
cGACCAGTGCCT‑CAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTg < 2:799097/132‑1 (MQ=255)
tCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAgg < 1:527548/71‑1 (MQ=255)
tCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAgg > 2:527548/1‑71 (MQ=255)
ccTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGt > 1:169570/1‑134 (MQ=255)
acaGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTcc < 2:506607/134‑1 (MQ=255)
acaGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTc < 2:909006/133‑1 (MQ=255)
gTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCCAGCAGGTc > 1:522965/1‑134 (MQ=255)
cAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCca > 1:924575/1‑124 (MQ=255)
cAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCca < 2:924575/124‑1 (MQ=255)
|
TCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCTTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGCGCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCCAGCAGGTC > AM260479/2593999‑2594252
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ 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
GCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCTTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGCGCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCCAGCAGGTCCTTGTCTTCGCCCTCG > AM260479/2593979‑2594268
|
GCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGG > GWNJ‑0478:712:GW2002102894th:2:1209:6662:75139/1‑150 (MQ=60)
CCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGC > GWNJ‑0478:712:GW2002102894th:2:2208:11566:65478/1‑150 (MQ=60)
GTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCG > GWNJ‑0478:712:GW2002102894th:2:1116:4297:27989/1‑148 (MQ=60)
GTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCG > GWNJ‑0478:712:GW2002102894th:2:2115:14483:68208/1‑148 (MQ=60)
GTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCT‑CAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGG > GWNJ‑0478:712:GW2002102894th:2:2203:1580:48771/1‑150 (MQ=60)
CTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCtgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:2109:14481:92927/1‑114 (MQ=60)
acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaggtgccTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCT < GWNJ‑0478:712:GW2002102894th:2:2101:11152:31594/96‑1 (MQ=60)
GGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCctgtctc > GWNJ‑0478:712:GW2002102894th:2:2204:11893:41893/1‑143 (MQ=60)
ACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTT < GWNJ‑0478:712:GW2002102894th:2:1103:1935:23289/150‑1 (MQ=60)
AGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTC > GWNJ‑0478:712:GW2002102894th:2:1110:6346:100472/1‑150 (MQ=60)
TGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCCAGCAGGTCC > GWNJ‑0478:712:GW2002102894th:2:1216:3687:96689/1‑150 (MQ=60)
CTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCCAGCAGGTCCTTG > GWNJ‑0478:712:GW2002102894th:2:2211:20387:57940/1‑150 (MQ=60)
GTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCCAGCAGGTCCTTGTCTTCGC > GWNJ‑0478:712:GW2002102894th:2:1216:18264:72184/1‑150 (MQ=60)
GTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCctgtctcttatacacatctcccgagcccacgagacggagc > GWNJ‑0478:712:GW2002102894th:2:2114:2201:12331/1‑110 (MQ=60)
|
GCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCTTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGCGCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGCGGCGACCAGGTCTTCCAGCAGGTCCTTGTCTTCGCCCTCG > AM260479/2593979‑2594268
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
