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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,153,816 |
T→C |
S84P (TCA→CCA) |
btuB → |
TonB‑dependent vitamin B12 receptor BtuB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,153,816 | 0 | T | C | 96.2%
| 74.9
/ ‑4.0
| 26 | S84P (TCA→CCA) | btuB | TonB‑dependent vitamin B12 receptor BtuB |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (10/15); total (10/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.47e-01 |
GACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGG > NZ_CP009273/4153729‑4153891
|
gACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCa < 1:395725/90‑1 (MQ=255)
tCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTAtt < 2:198445/90‑1 (MQ=255)
aCCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTcgc < 1:170672/90‑1 (MQ=255)
aCCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTcgc < 2:171238/90‑1 (MQ=255)
aCCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATCcgc < 1:298169/90‑1 (MQ=255)
tCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACaa < 2:46654/90‑1 (MQ=255)
gtgCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCCGGGCAGCTCCCCTCTATTTTTTTTTGCGGGACAAATGCCAGt > 1:368334/1‑90 (MQ=255)
gctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCa < 1:173589/90‑1 (MQ=255)
gctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCa < 2:139470/90‑1 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTTAGGTCAGCTCCCCTCTATTTTTTTTTGCGGGACAAATGCCAGTCAtgt > 2:417292/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTTGCGGTACAAATGCCCGTCAtgt > 2:26477/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCCTCTATTTTTTTTTGCGGGACAAAAGCCAGTCAtgt > 2:461273/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCAtgt > 1:13820/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTCGCGGGACAAATGCCAGTCAtgt > 1:262923/1‑90 (MQ=255)
gcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTTTTTTTTTTTGCGGGACAAAAGCCAGTCATgtgt > 2:217130/1‑90 (MQ=255)
gcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATgtgt < 1:417292/90‑1 (MQ=255)
gTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTgg > 1:128397/1‑90 (MQ=255)
ccGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTCGCGGGACAAAAGCCAGTCATGTGTTGGGGTTa > 2:195361/1‑90 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 2:190162/90‑1 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 1:195361/90‑1 (MQ=255)
tatCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGt < 2:522686/90‑1 (MQ=255)
tatCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGt < 1:286382/90‑1 (MQ=255)
cggTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGc > 1:225789/1‑90 (MQ=255)
ggTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCg < 1:398971/90‑1 (MQ=255)
gTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCgg < 2:128397/90‑1 (MQ=255)
gTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCgg < 1:63322/90‑1 (MQ=255)
|
GACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGG > NZ_CP009273/4153729‑4153891
|
| 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
CGTCAGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTG > NZ_CP009273/4153717‑4153906
|
CGTCAGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATACCACCCAAAACGGCGGTTCAGGGCAGCTCC > SRR3722088.591586/1‑100 (MQ=60)
AGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATC < SRR3722088.134581/100‑1 (MQ=60)
ATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTAT < SRR3722088.437094/100‑1 (MQ=60)
GACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTA < SRR3722088.399992/100‑1 (MQ=60)
ACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATG < SRR3722088.172394/100‑1 (MQ=60)
ACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATCCGCGGTACAAATG < SRR3722088.301072/100‑1 (MQ=60)
GGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCCGGGCAGCTCCCCTCTATTTTTTTTTGCGGGACAAATGCCAGT > SRR3722088.372248/1‑100 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGT > SRR3722088.13973/1‑100 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTCGCGGGACAAATGCCAGTCATGT > SRR3722088.265473/1‑100 (MQ=60)
GTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCCGGGCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGTGTTGG > SRR3722088.664491/1‑100 (MQ=60)
GTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGG > SRR3722088.129730/1‑100 (MQ=60)
GTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTTTTTGCGGTAAAAATGCCAGgccttggttgg > SRR3722088.332420/1‑89 (MQ=60)
GCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTG < SRR3722088.175333/100‑1 (MQ=60)
GCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAAT < SRR3722088.421922/100‑1 (MQ=60)
GTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCC < SRR3722088.197305/100‑1 (MQ=60)
TATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAAT < SRR3722088.289139/100‑1 (MQ=60)
CCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGC > SRR3722088.228044/1‑100 (MQ=60)
GGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTG < SRR3722088.403300/100‑1 (MQ=60)
GTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG < SRR3722088.63984/100‑1 (MQ=60)
GGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTG > SRR3722088.65059/1‑100 (MQ=60)
|
CGTCAGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTG > NZ_CP009273/4153717‑4153906
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
