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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,320,565 |
G→A |
Q521Q (CAG→CAA) |
yciQ → |
DUF2207 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,320,565 | 0 | G | A | 93.1%
| 96.6
/ ‑3.0
| 29 | Q521Q (CAG→CAA) | yciQ | DUF2207 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (2/0); new base A (7/20); total (9/20) |
| Fisher's exact test for biased strand distribution p-value = 8.87e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01 |
AGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGG > NZ_CP009273/1320478‑1320650
|
aGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGacaaca < 2:1453450/90‑1 (MQ=255)
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 2:383714/1‑90 (MQ=255)
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 1:1578875/1‑90 (MQ=255)
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCaa > 1:1046803/1‑90 (MQ=255)
ttATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTa < 1:1222234/90‑1 (MQ=255)
ttACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGccc < 1:164688/90‑1 (MQ=255)
ttACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGccc < 1:590060/90‑1 (MQ=255)
tACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCa < 1:1520708/90‑1 (MQ=255)
ccGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACg < 1:994273/90‑1 (MQ=255)
tGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGa > 2:1220200/1‑90 (MQ=255)
gTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGaa > 1:1247360/1‑90 (MQ=255)
ttGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGc < 2:904470/90‑1 (MQ=255)
ttGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGc < 2:61040/90‑1 (MQ=255)
ttGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGc < 1:864471/90‑1 (MQ=255)
tGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCg < 2:1115839/90‑1 (MQ=255)
tGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCg < 2:141069/90‑1 (MQ=255)
ggTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAAc < 2:1554989/90‑1 (MQ=255)
aCTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTgcg > 2:686665/1‑90 (MQ=255)
tGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 1:1298349/1‑49 (MQ=255)
tGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa < 2:1298349/49‑1 (MQ=255)
cATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTaa < 1:393715/90‑1 (MQ=255)
gTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgc < 2:480377/90‑1 (MQ=255)
gTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgc < 1:383714/90‑1 (MQ=255)
gTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgc < 1:1527918/90‑1 (MQ=255)
tatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgcagc < 2:868974/90‑1 (MQ=255)
tttttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCaa < 1:665072/90‑1 (MQ=255)
tttCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAaca > 2:1563250/1‑90 (MQ=255)
tttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAAc < 2:1171786/63‑1 (MQ=255)
tttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAAc > 1:1171786/1‑63 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGCTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac > 2:1574478/1‑90 (MQ=255)
cTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCAc > 1:1378324/1‑42 (MQ=255)
cTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCAc < 2:1378324/42‑1 (MQ=255)
aaCTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGaa < 1:675140/90‑1 (MQ=255)
gACAACAACGTCATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAgggg > 2:115853/1‑90 (MQ=255)
|
AGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGG > NZ_CP009273/1320478‑1320650
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ 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
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAACACGGAAACT > NZ_CP009273/1320469‑1320663
|
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAA > SRR3722078.1062465/1‑100 (MQ=60)
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAA > SRR3722078.1604574/1‑100 (MQ=60)
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAA < SRR3722078.65948/100‑1 (MQ=60)
TTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGT < SRR3722078.1241465/100‑1 (MQ=60)
TTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAA > SRR3722078.1267095/1‑100 (MQ=60)
TTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGC < SRR3722078.166605/100‑1 (MQ=60)
TTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGC < SRR3722078.596920/100‑1 (MQ=60)
TACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCT < SRR3722078.1545508/100‑1 (MQ=60)
CCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTAT < SRR3722078.1008736/100‑1 (MQ=60)
TTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAAC < SRR3722078.876044/100‑1 (MQ=60)
GTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCctgtctcttatacacatctgacgcggccgac > SRR3722078.1319022/1‑69 (MQ=60)
CATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCA < SRR3722078.398499/100‑1 (MQ=60)
GGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCctgtctcttatacacat > SRR3722078.1190020/1‑83 (MQ=60)
GTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTActgtctcttatacacatctgacgctgccgacgatggcg > SRR3722078.1400554/1‑62 (MQ=60)
GTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACAC < SRR3722078.1552811/100‑1 (MQ=60)
GTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACAC < SRR3722078.388392/100‑1 (MQ=60)
TTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGG < SRR3722078.672690/100‑1 (MQ=60)
AACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAACA < SRR3722078.682908/100‑1 (MQ=60)
AACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAACACGGAAACT < SRR3722078.600010/100‑1 (MQ=60)
|
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAACACGGAAACT > NZ_CP009273/1320469‑1320663
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
