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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,294,319 |
T→C |
D106G (GAT→GGT) |
ubiT ← |
SCP2 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,294,319 | 0 | T | C | 100.0%
| 32.6
/ NA
| 12 | D106G (GAT→GGT) | ubiT | SCP2 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/4); total (8/4) |
GTCCATCAGGTTTTTCACATACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGATCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCTAAC > NZ_CP009273/3294237‑3294398
|
gTCCATCAGGTTTTTCACATACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGttt > 2:446670/1‑90 (MQ=255)
tttttCACATACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCa > 2:375388/1‑90 (MQ=255)
ttttCACATACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCaa > 2:113598/1‑90 (MQ=255)
aTACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATcag > 1:167351/1‑90 (MQ=255)
gCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGAt > 2:335476/1‑90 (MQ=255)
gTATCGCCTTCAATCACCAGCCGACGCTGGCAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCg < 1:452426/90‑1 (MQ=255)
gTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCg < 1:346043/90‑1 (MQ=255)
gCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACt > 1:80501/1‑90 (MQ=255)
cAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAAc < 1:151801/90‑1 (MQ=255)
cAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATc < 1:335476/90‑1 (MQ=255)
gagCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCt > 2:292983/1‑90 (MQ=255)
cGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCTAAc > 1:246815/1‑90 (MQ=255)
|
GTCCATCAGGTTTTTCACATACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGATCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCTAAC > NZ_CP009273/3294237‑3294398
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
GGTTTTTCACATACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGATCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCTAACGACCAGTTTGCC > NZ_CP009273/3294245‑3294410
|
GGTTTTTCACATACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAG > SRR3722113.168707/1‑100 (MQ=60)
GCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACT > SRR3722113.81208/1‑100 (MQ=60)
GTATCGCCTTCAATCACCAGCCGACGCTGGCAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAAC < SRR3722113.457205/100‑1 (MQ=60)
GTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAAC < SRR3722113.349560/100‑1 (MQ=60)
CAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGC < SRR3722113.153063/100‑1 (MQ=60)
CAGCCGACGCTGGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCG < SRR3722113.338878/100‑1 (MQ=60)
GGAAGAAGAGCGTATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCTAAC > SRR3722113.248949/1‑100 (MQ=60)
TATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCTAACGACCAGTTTGCC > SRR3722113.270941/1‑100 (MQ=60)
TATCCGGACCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCTAACGACCAGTTTGCC > SRR3722113.321370/1‑100 (MQ=60)
|
GGTTTTTCACATACAGCCCCAGCTCCGTATCGCCTTCAATCACCAGCCGACGCTGGAAGAAGAGCGTATCCGGATCTTGTTTACGCGCCGCAATCATCAGCAGATCGCTGGCGTCGGCACTAAAACTCACATCAGCTTGCGCGTTCTGGCTAACGACCAGTTTGCC > NZ_CP009273/3294245‑3294410
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
