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 F2 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,180,586 |
(A)7→6 |
intergenic (+333/+77) |
yjaZ → / ← thiH |
heat‑shock protein C/2‑iminoacetate synthase ThiH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,180,580 | 0 | A | . | 95.2%
| 74.9
/ ‑1.1
| 21 | intergenic (+327/+83) | yjaZ/thiH | heat‑shock protein C/2‑iminoacetate synthase ThiH |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (6/14); total (6/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01 |
TTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCT > NZ_CP009273/4180492‑4180663
|
ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa > 2:539024/1‑90 (MQ=255)
tttttAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCt < 1:354010/90‑1 (MQ=255)
aGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac < 2:21249/90‑1 (MQ=255)
aaaCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac > 1:301521/1‑76 (MQ=255)
aaaCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac < 2:301521/76‑1 (MQ=255)
aCGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCa < 2:135279/90‑1 (MQ=255)
aGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCtt > 1:277689/1‑66 (MQ=255)
aGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCtt < 2:277689/66‑1 (MQ=255)
gCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGc < 1:539024/90‑1 (MQ=255)
gCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACC‑TGCGTTTTTCATCTTCCGTAGCg > 2:171664/1‑90 (MQ=255)
tttCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCt > 1:521015/1‑65 (MQ=255)
tttCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCt < 2:521015/65‑1 (MQ=255)
ccTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGaa < 1:37540/90‑1 (MQ=255)
ccTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGaa < 2:532328/90‑1 (MQ=255)
cTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAAt < 2:53727/90‑1 (MQ=255)
acaTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTa > 2:116096/1‑90 (MQ=255)
caTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTAc < 2:385920/90‑1 (MQ=255)
ttCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGt < 2:382064/90‑1 (MQ=255)
gctgACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCtt < 2:219779/90‑1 (MQ=255)
cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc < 1:288015/90‑1 (MQ=255)
gCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCg < 2:406364/90‑1 (MQ=255)
cTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGtct > 1:171153/1‑90 (MQ=255)
|
TTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCT > NZ_CP009273/4180492‑4180663
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGC > NZ_CP009273/4180487‑4180680
|
AGACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAC < SRR3722111.200907/100‑1 (MQ=60)
TTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACC < SRR3722111.358856/100‑1 (MQ=60)
AGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTctgt > SRR3722111.305426/1‑96 (MQ=60)
GGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTctgtctcttataca > SRR3722111.281160/1‑86 (MQ=60)
GGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTgtttcctgtctcttatacac > SRR3722111.529156/1‑80 (MQ=60)
GCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAAT < SRR3722111.547497/100‑1 (MQ=60)
CCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACG < SRR3722111.37977/100‑1 (MQ=60)
GCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCT > SRR3722111.173291/1‑100 (MQ=60)
CGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAG < SRR3722111.291680/100‑1 (MQ=60)
CCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCG < SRR3722111.480247/100‑1 (MQ=60)
AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATctgtctcttatacacatctgacgc > SRR3722111.30143/1‑76 (MQ=60)
|
AGACTTTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCGTCTCATAGTCTTTGCGAGGC > NZ_CP009273/4180487‑4180680
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
