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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,678,723 |
A→C |
G48G (GGT→GGG) |
glyA ← |
serine hydroxymethyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,678,723 | 0 | A | C | 100.0%
| 34.1
/ NA
| 12 | G48G (GGT→GGG) | glyA | serine hydroxymethyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (3/9); total (3/9) |
TCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTG > NZ_CP009273/2678643‑2678806
|
taaaCAATACCAACATCCCCCAACCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGcc < 1:31043/88‑1 (MQ=255)
atCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTAc > 2:234874/1‑90 (MQ=255)
ccccGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGc < 2:115582/87‑1 (MQ=255)
ccgccgTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAg < 1:141309/90‑1 (MQ=255)
ccgccgTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAg < 2:27221/90‑1 (MQ=255)
tAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGAtg < 2:98849/90‑1 (MQ=255)
cAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCtt > 1:143608/1‑90 (MQ=255)
tgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACtt > 1:172457/1‑90 (MQ=255)
tgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACtt < 2:23493/90‑1 (MQ=255)
aGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTcc < 1:234874/90‑1 (MQ=255)
gCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCt < 2:36189/90‑1 (MQ=255)
cTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTg < 2:114753/90‑1 (MQ=255)
|
TCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTG > NZ_CP009273/2678643‑2678806
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ 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
CGATCGATCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAG > NZ_CP009273/2678625‑2678814
|
cgatcgaccgccttttttccaacaatataaacatcccccaacCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACC < SRR3722076.131648/58‑1 (MQ=60)
tttttcaaacaataacaacatccccccacCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCAT < SRR3722076.244071/71‑1 (MQ=60)
taaacaataccaacatcccccaacCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGC < SRR3722076.31411/76‑1 (MQ=60)
acatcccccCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGT < SRR3722076.194370/91‑1 (MQ=60)
atcccccaagCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAG < SRR3722076.238526/90‑1 (MQ=60)
CCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGG < SRR3722076.142951/100‑1 (MQ=60)
GGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTT > SRR3722076.145265/1‑100 (MQ=60)
GCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTT > SRR3722076.174620/1‑100 (MQ=60)
AGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAG < SRR3722076.238130/100‑1 (MQ=60)
|
CGATCGATCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAG > NZ_CP009273/2678625‑2678814
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
