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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,713,202 |
A→G |
intergenic (+74/‑207) |
yiaG → / → cspA |
HTH‑type transcriptional regulator/RNA chaperone/antiterminator CspA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,713,202 | 0 | A | G | 76.9%
| 42.5
/ 0.5
| 26 | intergenic (+74/‑207) | yiaG/cspA | HTH‑type transcriptional regulator/RNA chaperone/antiterminator CspA |
| Reads supporting (aligned to +/- strand): ref base A (0/6); new base G (13/7); total (13/13) |
| Fisher's exact test for biased strand distribution p-value = 1.49e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTGTAGTA > NZ_CP009273/3713123‑3713285
|
gAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAAttg > 2:73743/1‑90 (MQ=255)
aaTAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAAttgt > 1:119439/1‑90 (MQ=255)
aTTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGt < 1:3215/90‑1 (MQ=255)
tGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCtt > 1:444903/1‑90 (MQ=255)
gTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTgg < 1:325560/86‑1 (MQ=255)
gTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTgg > 2:325560/1‑86 (MQ=255)
cTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCa > 1:322466/1‑90 (MQ=255)
cTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCa > 2:399441/1‑90 (MQ=255)
gatgaCAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAAc > 1:372964/1‑90 (MQ=255)
aCAGGACCGTTTTCCACCCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGtt < 1:297767/90‑1 (MQ=255)
cAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGttt > 1:398964/1‑90 (MQ=255)
cAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGttt > 2:107831/1‑90 (MQ=255)
aGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCCCCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTg < 1:74508/90‑1 (MQ=255)
ggACCTTTTTCCAACCGATTAATCAAAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGa < 2:76322/90‑1 (MQ=255)
ggACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGa > 2:294756/1‑90 (MQ=255)
ccGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGt > 1:167266/1‑90 (MQ=255)
tttttCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTAc < 1:451465/89‑1 (MQ=255)
tttttCCAACCGATTAATCAAAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTAc < 2:192361/89‑1 (MQ=255)
ttCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGa > 2:168911/1‑90 (MQ=255)
ttCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCACCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGa < 2:448432/90‑1 (MQ=255)
gATAAATCATAAATATGAAAAATAATTTTTGCACCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTaaa < 2:372964/90‑1 (MQ=255)
ttAATCATAAATATGAAAAATATTTGTTGCATCCCCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGc < 2:337521/90‑1 (MQ=255)
aaTCATAAATATGGAAAATAATTGTTGCATCACACGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAg < 1:450468/90‑1 (MQ=255)
aaTATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTgtagta > 2:133056/1‑90 (MQ=255)
aaTATGAAAAATAATTGTTGCATCCCCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTgtagta < 2:453377/90‑1 (MQ=255)
atGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTg < 1:122457/59‑1 (MQ=255)
|
GAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTGTAGTA > NZ_CP009273/3713123‑3713285
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAGTTGATGGAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTGTAGTAAGG > NZ_CP009273/3713114‑3713288
|
CAGTTGATGGAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGT > SRR3722113.120464/1‑100 (MQ=60)
GCTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTT > SRR3722113.449613/1‑100 (MQ=60)
ATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGC < SRR3722113.3250/100‑1 (MQ=60)
TGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCCCCCGCCAATGCGTGGCTTAATGCAC < SRR3722113.328800/100‑1 (MQ=60)
GTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCA > SRR3722113.325657/1‑100 (MQ=60)
TTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAAC > SRR3722113.376836/1‑100 (MQ=60)
GTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTT > SRR3722113.403137/1‑100 (MQ=60)
GATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGT > SRR3722113.168621/1‑100 (MQ=60)
ACAGGACCGTTTTCCACCCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAG < SRR3722113.300576/100‑1 (MQ=60)
ggagatgtgtataagagacagAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGAC < SRR3722113.123506/79‑1 (MQ=60)
AGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCCCCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGAC < SRR3722113.75160/100‑1 (MQ=60)
TTTTTCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAA < SRR3722113.456236/100‑1 (MQ=60)
AATCATAAATATGGAAAATAATTGTTGCATCACACGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTGTAGTAAGG < SRR3722113.455234/100‑1 (MQ=60)
|
CAGTTGATGGAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTGTAGTAAGG > NZ_CP009273/3713114‑3713288
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
