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 I75 R1
|
71 |
32.8 |
2150506 |
93.3% |
2006422 |
83.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,935,432 |
G→A |
noncoding (265/1542 nt) |
BW25113_RS19520 → |
16S ribosomal RNA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,935,432 | 0 | G | A | 91.7%
| 48.7
/ ‑1.9
| 24 | noncoding (265/1542 nt) | BW25113_RS19520 | 16S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (7/15); total (8/16) |
| 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 |
ATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCC > NZ_CP009273/3935346‑3935479
|
aTAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCt > 1:136474/1‑90 (MQ=18)
tCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTa > 2:162097/1‑90 (MQ=18)
cGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAg < 2:100693/90‑1 (MQ=25)
aGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcga < 1:175158/90‑1 (MQ=18)
gACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac < 2:741373/90‑1 (MQ=18)
gACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac < 2:646716/90‑1 (MQ=18)
gACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac < 1:314933/90‑1 (MQ=18)
gACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac < 1:767603/90‑1 (MQ=18)
aCCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgacg < 1:991405/90‑1 (MQ=18)
aCCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGATCACCTAGGcgacg < 1:982478/90‑1 (MQ=255)
ccAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgacga < 1:500706/90‑1 (MQ=18)
ggggACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGc > 2:978770/1‑90 (MQ=25)
gggACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCt > 2:695219/1‑90 (MQ=33)
gggACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCt < 1:303808/90‑1 (MQ=18)
ccTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTc > 1:297984/1‑90 (MQ=25)
ttCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGGGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTg > 2:839665/1‑90 (MQ=255)
gggCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTgaga < 1:54012/90‑1 (MQ=18)
gCCTCTTGCCATCAGATGTGCACAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAgg > 1:135917/1‑90 (MQ=255)
ctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac < 1:47321/64‑1 (MQ=255)
ctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGcgac > 2:47321/1‑64 (MQ=255)
tGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGAGACGATCCCTAGCTGGTCTGAGAGGATGAcc < 1:693292/90‑1 (MQ=255)
aTCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGcc < 1:695219/90‑1 (MQ=33)
aTCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGcc < 2:469929/90‑1 (MQ=18)
aTCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACAGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGcc < 2:969848/90‑1 (MQ=18)
|
ATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCC > NZ_CP009273/3935346‑3935479
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCTTCATCCCGAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGTCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTATCATCACCACGATT > NZ_CP009273/4004279‑4004462
|
CCTTCATCCCGAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCA > SRR3722213.1089984/1‑100 (MQ=60)
CCTTCATCCCGAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCA > SRR3722213.899485/1‑100 (MQ=60)
TCCCGAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTC < SRR3722213.905102/100‑1 (MQ=60)
GAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACC < SRR3722213.999181/100‑1 (MQ=60)
AGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCT > SRR3722213.127310/1‑100 (MQ=60)
GGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATA > SRR3722213.632137/1‑100 (MQ=60)
GAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATAC < SRR3722213.589551/100‑1 (MQ=60)
TGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCG > SRR3722213.106839/1‑100 (MQ=60)
GATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACctgtc > SRR3722213.535116/1‑95 (MQ=60)
GATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACctgtc > SRR3722213.222063/1‑95 (MQ=60)
GTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAA > SRR3722213.678902/1‑100 (MQ=60)
GTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAA > SRR3722213.758444/1‑100 (MQ=60)
GCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACC < SRR3722213.232520/100‑1 (MQ=60)
acaGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATC < SRR3722213.690136/97‑1 (MQ=60)
GTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAG > SRR3722213.842888/1‑100 (MQ=60)
gatgtgtataagagacagCTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGT < SRR3722213.119734/82‑1 (MQ=60)
GCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTT > SRR3722213.39901/1‑100 (MQ=60)
ATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCAT < SRR3722213.87161/100‑1 (MQ=60)
GCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATGAAAGAGctgtctcttata > SRR3722213.942586/1‑88 (MQ=60)
GCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTG > SRR3722213.497101/1‑100 (MQ=60)
CTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTAC > SRR3722213.27495/1‑100 (MQ=60)
CTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTAC < SRR3722213.240132/100‑1 (MQ=60)
TCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACT < SRR3722213.160283/100‑1 (MQ=60)
CTATTTATCGTAATCGTTCTTTATTTGGCCGGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTT > SRR3722213.408683/1‑100 (MQ=60)
TTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTATCA < SRR3722213.766016/100‑1 (MQ=60)
ATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGTCGCTACTTATCATC < SRR3722213.638910/100‑1 (MQ=60)
GTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGctgtctcttatacacatctccgagcccacgagacccgttattatatcg > SRR3722213.397620/1‑52 (MQ=60)
|
CCTTCATCCCGAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGTCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTATCATCACCACGATT > NZ_CP009273/4004279‑4004462
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
