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 |
|
A2 F5 I176 R1
|
180 |
42.9 |
1710034 |
96.5% |
1650182 |
119.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
633,831 |
C→T |
A67T (GCT→ACT) |
dsbG ← |
thiol:disulfide interchange protein DsbG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 633,831 | 0 | C | T | 100.0%
| 90.0
/ NA
| 24 | A67T (GCT→ACT) | dsbG | thiol:disulfide interchange protein DsbG |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (7/17); total (7/17) |
GAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTG > NZ_CP009273/633706‑633962
|
gaggagCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATc < 2:336809/138‑1 (MQ=255)
gCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGt < 2:571085/139‑1 (MQ=255)
agggggATTGTTCCATCCGTTGCCACATTTCGCGTCCTGAGGGGGCGTCACATTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAg > 1:282344/4‑139 (MQ=255)
aGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAg > 2:326077/1‑139 (MQ=255)
ttCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTg < 1:171222/139‑1 (MQ=255)
ccATCCGTTGCCACCTTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGCGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGa < 2:608037/138‑1 (MQ=255)
ccATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGa < 1:326077/138‑1 (MQ=255)
ccATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGa < 2:677141/138‑1 (MQ=255)
cGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCa < 2:547165/139‑1 (MQ=255)
tGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCatat > 2:685492/1‑139 (MQ=255)
gCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGt < 2:854507/98‑1 (MQ=255)
gCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGt > 1:854507/1‑98 (MQ=255)
gCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGAt < 2:348276/139‑1 (MQ=255)
gCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGAt < 1:562297/139‑1 (MQ=255)
cTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATTTTGTGTCTGGTAGATGGTGATGCTCATATCCTGATACTTTCCGAGATa < 2:282344/139‑1 (MQ=255)
gTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAAcc < 1:259434/139‑1 (MQ=255)
aGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGa < 2:15134/139‑1 (MQ=255)
aGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGa < 1:685492/139‑1 (MQ=255)
ttACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAg > 2:352408/1‑72 (MQ=255)
ttACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAg < 1:352408/72‑1 (MQ=255)
aGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTtgatga > 2:372350/1‑139 (MQ=255)
tACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCaa < 2:754080/139‑1 (MQ=255)
tACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCa < 1:66272/138‑1 (MQ=255)
gagaTAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTg > 1:658387/1‑139 (MQ=255)
|
GAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTG > NZ_CP009273/633706‑633962
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACCGGCGCATCTTTTTTACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGGAAGTTCCT > NZ_CP009273/633683‑633977
|
tcaagcagaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTG < SRR3722130.59111/83‑1 (MQ=60)
TTTTTACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATC < SRR3722130.611262/149‑1 (MQ=60)
GTCGAGGAGCCAGGGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCTGAGGGGGCGTCACATTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGG > SRR3722130.286702/1‑151 (MQ=60)
gacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCC < SRR3722130.357889/94‑1 (MQ=60)
GTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATC < SRR3722130.173791/151‑1 (MQ=60)
TCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCC < SRR3722130.331120/150‑1 (MQ=60)
TTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGctgtctcttatacacatctccgagcccacg > SRR3722130.866827/1‑120 (MQ=60)
GGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATT < SRR3722130.570800/151‑1 (MQ=60)
GGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTC < SRR3722130.263482/151‑1 (MQ=60)
AAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATG < SRR3722130.695663/151‑1 (MQ=60)
ACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCtgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaaaacctcgtcagacac > SRR3722130.519426/1‑54 (MQ=60)
gagatgtgtataagagacaGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTC < SRR3722130.585779/132‑1 (MQ=60)
GTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTAC < SRR3722130.67204/150‑1 (MQ=60)
ACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGG > SRR3722130.668223/1‑151 (MQ=60)
GAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGGAAGTT > SRR3722130.23952/1‑151 (MQ=60)
ATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGGAAGTTCCT > SRR3722130.114627/1‑151 (MQ=60)
|
ACCGGCGCATCTTTTTTACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGGAAGTTCCT > NZ_CP009273/633683‑633977
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
