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 |
3,848,051 |
T→G |
F257C (TTT→TGT) |
emrD → |
multidrug efflux MFS transporter EmrD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,848,051 | 0 | T | G | 91.8%
| 144.1
/ 3.4
| 49 | F257C (TTT→TGT) | emrD | multidrug efflux MFS transporter EmrD |
| Reads supporting (aligned to +/- strand): ref base T (3/1); new base G (32/13); total (35/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.58e-01 |
GGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCT > NZ_CP009273/3847972‑3848137
|
ggCGTGCTGATGGGCGCGGTGTTAGGGCTGGGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGGGCa > 1:1200399/1‑90 (MQ=255)
cGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATg < 2:1468793/90‑1 (MQ=255)
gTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATgg > 1:453536/1‑90 (MQ=255)
gTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGgcgc > 2:835858/1‑86 (MQ=255)
gTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGgcgc < 1:835858/86‑1 (MQ=255)
gggCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCgg < 1:938743/90‑1 (MQ=255)
gcgGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGt > 1:725001/1‑90 (MQ=255)
cgGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTc < 2:941886/90‑1 (MQ=255)
cgGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTc > 1:320271/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:219298/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:1244722/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:1547419/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt < 2:1492318/90‑1 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:1280263/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:520997/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:1459536/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:669174/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:1578122/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:1492318/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:157882/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:871413/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:219408/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:192120/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:930680/1‑90 (MQ=255)
gTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCa > 2:855143/1‑90 (MQ=255)
gTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCa > 2:658445/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:640710/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 2:181338/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:1228276/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:1243128/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 2:691081/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:390991/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:71141/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:704903/1‑90 (MQ=255)
tttGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTc < 2:1265444/90‑1 (MQ=255)
tttGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTc < 1:520997/90‑1 (MQ=255)
ttGGTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCg > 1:808234/1‑90 (MQ=255)
tttATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGtt < 2:157882/90‑1 (MQ=255)
tATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTc < 1:977064/50‑1 (MQ=255)
tATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTc > 2:977064/1‑50 (MQ=255)
tATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTAt > 2:781837/1‑90 (MQ=255)
tCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATctg < 2:640710/90‑1 (MQ=255)
gCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATctgctg < 1:930680/90‑1 (MQ=255)
ccGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCtgctgc > 2:1221229/1‑90 (MQ=255)
aGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGctggctgg < 2:390991/90‑1 (MQ=255)
gCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCtggctggc > 2:1508739/1‑90 (MQ=255)
cGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTtctc < 2:1545103/46‑1 (MQ=255)
cGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTtctc > 1:1545103/1‑46 (MQ=255)
cGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTggctggct < 1:938048/90‑1 (MQ=255)
|
GGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCT > NZ_CP009273/3847972‑3848137
|
| 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
TTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGGAT > NZ_CP009273/3847958‑3848150
|
TTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGG < SRR3722078.1273198/100‑1 (MQ=60)
AGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGGGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGGGCA > SRR3722078.1219230/1‑100 (MQ=60)
CTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGG > SRR3722078.458955/1‑100 (MQ=60)
CGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCC < SRR3722078.846984/100‑1 (MQ=60)
GCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGT > SRR3722078.734030/1‑100 (MQ=60)
CTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTC > SRR3722078.324192/1‑100 (MQ=60)
GGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAAT < SRR3722078.951771/100‑1 (MQ=60)
tcggcagcgtcagatgtgtataagagacagGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACG < SRR3722078.991114/70‑1 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722078.159725/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722078.1483345/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722078.1516651/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722078.1572627/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722078.713429/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722078.1247626/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722078.1262776/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722078.71980/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722078.648081/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722078.395748/1‑100 (MQ=60)
GGTCAGTATTTTGGTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCG > SRR3722078.818904/1‑100 (MQ=60)
TTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGC < SRR3722078.527160/100‑1 (MQ=60)
GCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCT < SRR3722078.943502/100‑1 (MQ=60)
ATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGctgtctcttatacacatctgacgctgccgacgat > SRR3722078.1570281/1‑66 (MQ=60)
GCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGA > SRR3722078.234872/1‑100 (MQ=60)
CGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTG < SRR3722078.951058/100‑1 (MQ=60)
GTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGGGGCAGTCGGTTATCTGCctgtctcttatacacatctgacgctgccg > SRR3722078.1051619/1‑71 (MQ=60)
|
TTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGGAT > NZ_CP009273/3847958‑3848150
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
