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 |
|
A0 F0 I1 R1
|
61 |
39.0 |
4165548 |
97.4% |
4057243 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,110,662 |
A→G |
E31E (GAA→GAG) |
vgrG → |
type VI secretion system tip protein VgrG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,110,662 | 0 | A | G | 100.0%
| 13.6
/ NA
| 8 | E31E (GAA→GAG) | vgrG | type VI secretion system tip protein VgrG |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (3/5); total (3/5) |
GCGGCCAGCAAAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAC > NC_017635/3110616‑3110706
|
gcgGCCAGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGagca < 2:352913/49‑1 (MQ=11)
gCCAGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGCAACTg < 2:630568/50‑1 (MQ=11)
aGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGCAACTGAg > 2:928805/1‑49 (MQ=11)
gACCTTTGAAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATc > 2:518510/1‑49 (MQ=14)
aCCTTTGAAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATcc < 2:1216163/49‑1 (MQ=14)
ccTTTGAAGGCCGCGAGCAACTTAGTACCCCGTTCCGCTACGATATCCAg < 1:1462026/50‑1 (MQ=17)
tgAAGTCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTa > 2:1286186/2‑50 (MQ=17)
ccGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTa < 2:277143/50‑1 (MQ=255)
cgcgAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAc < 1:27030/50‑1 (MQ=255)
|
GCGGCCAGCAAAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAC > NC_017635/3110616‑3110706
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCGCGGCCAGCAAAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAC > NC_017635/3110614‑3110706
|
TCGCGGCCAGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGC < M01420:85:000000000‑AC936:1:1107:8641:26338/50‑1 (MQ=16)
AGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGCAACTGAGTA < M01420:85:000000000‑AC936:1:1109:14756:3710/51‑1 (MQ=0)
AGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGCAACTGAGTA < M01420:85:000000000‑AC936:1:1109:21700:2672/51‑1 (MQ=0)
CAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGCAACTGAGTACC < M01420:85:000000000‑AC936:1:1112:6199:22208/51‑1 (MQ=0)
AAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCC < M01420:85:000000000‑AC936:1:2106:12872:9364/51‑1 (MQ=0)
CCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGCAACTGAGTACCCCGTT < M01420:85:000000000‑AC936:1:1104:8614:15671/50‑1 (MQ=0)
GGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCT < M01420:85:000000000‑AC936:1:1102:9638:13063/50‑1 (MQ=0)
GGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCT > M01420:85:000000000‑AC936:1:2113:24494:14722/1‑50 (MQ=0)
GATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTAC < M01420:85:000000000‑AC936:1:2106:17556:5638/51‑1 (MQ=0)
ACCTTTGAAGGCCGCGAGCAACTTAGTACCCCGTTCCGCTACGATATCCAG < M01420:85:000000000‑AC936:1:2106:12212:22253/51‑1 (MQ=47)
CCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAC < M01420:85:000000000‑AC936:1:1101:24760:12339/51‑1 (MQ=39)
|
TCGCGGCCAGCAAAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAC > NC_017635/3110614‑3110706
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
