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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,313,652 |
C→G |
A132P (GCC→CCC) |
trpCF ← |
bifunctional indole‑3‑glycerol‑phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,313,652 | 0 | C | G | 100.0%
| 44.6
/ NA
| 15 | A132P (GCC→CCC) | trpCF | bifunctional indole‑3‑glycerol‑phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (9/6); total (9/6) |
CCCATCTCCAGACTGTGAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGCCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGCTGCGGGGC > NZ_CP009273/1313567‑1313724
|
cccATCTCCAGACTGTGAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTgg > 2:613416/1‑90 (MQ=255)
gtgAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCag > 1:420754/1‑90 (MQ=255)
gtgAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCag > 1:48326/1‑90 (MQ=255)
gtgAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCag > 2:569557/1‑90 (MQ=255)
gAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCagat < 1:543804/90‑1 (MQ=255)
gAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCagat < 2:432961/90‑1 (MQ=255)
gAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCagat < 2:521023/90‑1 (MQ=255)
gAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCagat > 2:543804/1‑90 (MQ=255)
gAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCagat < 2:70501/90‑1 (MQ=255)
cTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTc < 1:112434/90‑1 (MQ=255)
ttGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGaa < 2:577452/90‑1 (MQ=255)
tcATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTa > 1:264643/1‑90 (MQ=255)
gAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGc > 1:326581/1‑90 (MQ=255)
cATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGCTGCgg > 1:646312/1‑90 (MQ=255)
taataaGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGCTGCGGGGc > 1:577475/1‑90 (MQ=255)
|
CCCATCTCCAGACTGTGAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGCCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGCTGCGGGGC > NZ_CP009273/1313567‑1313724
|
| 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
CACCCCCATCTCCAGACTGTGAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGCCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGCTGCGGGGC > NZ_CP009273/1313563‑1313724
|
CACCCCCATCTCCAGACTGTGAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAG < SRR3722088.593208/100‑1 (MQ=60)
TCTCCAGACTGTGAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAG > SRR3722088.425439/1‑100 (MQ=60)
TCTCCAGACTGTGAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAG > SRR3722088.48830/1‑100 (MQ=60)
GAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTA < SRR3722088.550435/100‑1 (MQ=60)
CTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAG < SRR3722088.113602/100‑1 (MQ=60)
ATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTA > SRR3722088.267208/1‑100 (MQ=60)
ATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGC > SRR3722088.329941/1‑100 (MQ=60)
GTACTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGCTGCGG > SRR3722088.654322/1‑100 (MQ=60)
CTGAAAGCATTAATAAGCAGGCATCGGGCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGCTGCGGGGC > SRR3722088.584557/1‑100 (MQ=60)
|
CACCCCCATCTCCAGACTGTGAGCGACGGCGGCAAGCTGGCGATATTGGTCGTCATCCAGTACTGAAAGCATTAATAAGCAGGCATCGGCCTGGTAATAGCGCGCCAGATAGATCTGGTAAGGGTCGATAATGAAGTCTTTACATAAAATCGGCTGCGGGGC > NZ_CP009273/1313563‑1313724
|
| 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: ‑ |
