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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 84.2%
| 48.9
/ 3.2
| 19 | G48G (GGT→GGG) | glyA | serine hydroxymethyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (2/1); new base C (11/5); total (13/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTC > NZ_CP009273/2678638‑2678803
|
gttgttCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCt > 2:626797/1‑90 (MQ=255)
gttCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAG‑ACCCTgtct > 1:811822/1‑87 (MQ=255)
gttCAACAATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTgcg > 2:66403/1‑90 (MQ=255)
cAACGAAATCAACATCCCCCCACCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCt < 2:697768/90‑1 (MQ=255)
atCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTAc > 1:571342/1‑90 (MQ=255)
cTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCt < 1:22625/90‑1 (MQ=255)
cTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCt > 1:375316/1‑90 (MQ=255)
tCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTg > 1:20987/1‑90 (MQ=255)
gTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGa > 1:687062/1‑90 (MQ=255)
gTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGa > 2:598301/1‑90 (MQ=255)
ttGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATc > 1:541947/1‑90 (MQ=255)
tGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGAt < 2:374328/88‑1 (MQ=255)
tGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGAt > 1:374328/1‑88 (MQ=255)
ggATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCg > 1:388295/1‑90 (MQ=255)
gttgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTAc < 1:661970/90‑1 (MQ=255)
tgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACtt < 1:415935/90‑1 (MQ=255)
tgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACtt < 1:96721/90‑1 (MQ=255)
tgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACtt > 1:35177/1‑90 (MQ=255)
cAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTc > 2:625292/1‑90 (MQ=255)
|
GTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTC > NZ_CP009273/2678638‑2678803
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
CGATCGATCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > NZ_CP009273/2678625‑2678815
|
cgatcgaccccagtttttccaacaatataAACATCCTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAAC < SRR3722079.87104/71‑1 (MQ=60)
cgaccgttcgccatttgttcaccgatataatcttccacgcatCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACC < SRR3722079.21535/58‑1 (MQ=60)
CGATCGCTCCCCAGTTTTTCAACGATATCAACATCCTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACC < SRR3722079.148654/100‑1 (MQ=60)
CGATCGATCGCCAGTTTTTCAACAATATCAACATCCTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACC < SRR3722079.349174/100‑1 (MQ=60)
CGATCGACCGCCAGTTGTTAAACGATATAAACATCCTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACC < SRR3722079.140416/100‑1 (MQ=60)
ATCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCG > SRR3722079.700622/1‑100 (MQ=60)
GTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTAC > SRR3722079.576953/1‑100 (MQ=60)
TATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCT > SRR3722079.378356/1‑100 (MQ=60)
ATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTG > SRR3722079.21132/1‑100 (MQ=60)
aaatcctccCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGT < SRR3722079.443181/91‑1 (MQ=60)
CCCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTT < SRR3722079.22786/100‑1 (MQ=60)
CCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGA > SRR3722079.694283/1‑100 (MQ=60)
GTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATC > SRR3722079.547081/1‑100 (MQ=60)
TAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCA > SRR3722079.377358/1‑100 (MQ=60)
GCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCG > SRR3722079.391501/1‑100 (MQ=60)
GCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTT > SRR3722079.35434/1‑100 (MQ=60)
GTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGC < SRR3722079.668850/100‑1 (MQ=60)
TGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTC < SRR3722079.97483/100‑1 (MQ=60)
TGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTC < SRR3722079.419511/100‑1 (MQ=60)
GCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > SRR3722079.830872/1‑100 (MQ=60)
GCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > SRR3722079.425918/1‑100 (MQ=60)
|
CGATCGATCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > NZ_CP009273/2678625‑2678815
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
