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 I175 R1
|
221 |
18.5 |
1047116 |
95.1% |
995807 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,590,291 |
T→C |
I168V (ATC→GTC) |
dnaC ← |
DNA replication protein DnaC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,590,291 | 0 | T | C | 100.0%
| 102.6
/ NA
| 29 | I168V (ATC→GTC) | dnaC | DNA replication protein DnaC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/21); total (8/21) |
TTGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGATCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGCC > NZ_CP009273/4590209‑4590373
|
ttGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACcagc < 2:277281/90‑1 (MQ=255)
ttGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACcagc < 1:300402/90‑1 (MQ=255)
agaagaGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGaac < 2:84830/90‑3 (MQ=255)
agagCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAAc > 1:299260/1‑90 (MQ=255)
gagCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACg > 1:173345/1‑90 (MQ=255)
agCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGt < 1:158467/90‑1 (MQ=255)
agCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGt < 1:511113/90‑1 (MQ=255)
ggcgATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGc > 2:408686/1‑90 (MQ=255)
gATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCa < 1:521801/90‑1 (MQ=255)
tCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTaa < 1:294294/90‑1 (MQ=255)
tCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTaa < 1:408686/90‑1 (MQ=255)
tgatCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAgt < 1:478169/86‑1 (MQ=255)
tgatCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAgt > 2:478169/1‑86 (MQ=255)
atCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATc > 1:479828/1‑59 (MQ=255)
atCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATc < 2:479828/59‑1 (MQ=255)
atCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGttct < 1:338510/90‑1 (MQ=255)
cACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGttcttc > 1:198663/1‑90 (MQ=255)
tCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTAt < 2:395443/90‑1 (MQ=255)
gCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCttt > 2:152348/1‑90 (MQ=255)
ccGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTc < 1:244933/90‑1 (MQ=255)
cGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCa > 1:257662/1‑90 (MQ=255)
tcATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGcc < 2:386181/90‑1 (MQ=255)
tcATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGcc < 2:299260/90‑1 (MQ=255)
tcATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGcc < 2:257662/90‑1 (MQ=255)
tcATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGcc < 2:198663/90‑1 (MQ=255)
tcATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGcc < 2:193787/90‑1 (MQ=255)
tcATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGcc < 2:485094/90‑1 (MQ=255)
tcATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGcc < 2:70942/90‑1 (MQ=255)
tcATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGcc < 1:442129/90‑1 (MQ=255)
|
TTGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGATCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGCC > NZ_CP009273/4590209‑4590373
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ 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
GTTTGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGATCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGCCGACATAATATC > NZ_CP009273/4590207‑4590384
|
GTTTGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAAC > SRR3722048.303740/1‑100 (MQ=60)
TTTGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACG > SRR3722048.175839/1‑100 (MQ=60)
TTGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGT < SRR3722048.304899/100‑1 (MQ=60)
AGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATC < SRR3722048.160735/100‑1 (MQ=60)
AGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATC < SRR3722048.519561/100‑1 (MQ=60)
GATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAG < SRR3722048.530436/100‑1 (MQ=60)
TCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTC < SRR3722048.298700/100‑1 (MQ=60)
TCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTC < SRR3722048.415319/100‑1 (MQ=60)
CTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCctgtctcttatacacatctcc > SRR3722048.487771/1‑79 (MQ=60)
GGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTC > SRR3722048.201447/1‑100 (MQ=60)
TTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGC < SRR3722048.486088/100‑1 (MQ=60)
ATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTAC < SRR3722048.343762/100‑1 (MQ=60)
GTCTGCACGCCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCA > SRR3722048.261405/1‑100 (MQ=60)
CCGATCTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGCCGACA < SRR3722048.248431/100‑1 (MQ=60)
CTCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGCCGACATAATA > SRR3722048.466506/1‑100 (MQ=60)
TCATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGCCGACATAATAT < SRR3722048.449382/100‑1 (MQ=60)
CATCGACCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCctgtctcttatacacat > SRR3722048.302662/1‑83 (MQ=60)
|
GTTTGGAAGAAGAGCGGCGATCGACGATCTGGTTGATGATCACTTTTTCGTATTTCGATTCGGTCTGCACGCCGATCTCATCGATCACCAGCAGATCAACGTTGCTCAGATCGTTAAGCAGTTGTTCTTCGCTGGTACCGCTATTCCTGAAGGTATCTTTCATCGCCGACATAATATC > NZ_CP009273/4590207‑4590384
|
| 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: ‑ |
