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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,013,755 |
G→C |
R63P (CGC→CCC) |
fliM → |
flagellar motor switch protein FliM |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,013,755 | 0 | G | C | 92.9%
| 38.7
/ ‑2.7
| 14 | R63P (CGC→CCC) | fliM | flagellar motor switch protein FliM |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (6/7); total (6/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-01 |
TCGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCAT > NZ_CP009273/2013672‑2013824
|
tCGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCAttt > 1:149341/1‑90 (MQ=255)
cGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCAtttt < 2:320523/90‑1 (MQ=255)
cGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCAtttc < 1:563060/90‑2 (MQ=255)
gTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTAt > 1:530758/1‑90 (MQ=255)
gATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTCTGCCCCCCATTTTCGTATgggg < 2:356635/90‑1 (MQ=255)
aTCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGc > 1:26590/1‑90 (MQ=255)
ccAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACct > 1:109508/1‑90 (MQ=255)
cAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACctg > 2:337050/1‑90 (MQ=255)
acgacgGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACctgct > 2:483263/1‑90 (MQ=255)
gTTGTGCGCGACCTTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGcgtcgt < 2:522510/90‑1 (MQ=255)
gTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACCTGCTGcgtcgt < 2:398780/90‑1 (MQ=255)
tgCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGcc < 1:303559/90‑1 (MQ=255)
gAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGat < 1:540459/90‑1 (MQ=255)
cATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCAt < 1:287437/90‑1 (MQ=255)
|
TCGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCAT > NZ_CP009273/2013672‑2013824
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
AAAGTGACATTCGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTAC > NZ_CP009273/2013662‑2013834
|
AAAGTGACATTCGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTT > SRR3722112.151189/1‑100 (MQ=60)
ACATTCGTTCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTAT > SRR3722112.538628/1‑100 (MQ=60)
CGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGC > SRR3722112.26927/1‑100 (MQ=60)
CGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTCCGTATGGGGC < SRR3722112.571605/100‑1 (MQ=60)
ATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACCT > SRR3722112.110868/1‑100 (MQ=60)
TGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAAC < SRR3722112.307046/100‑1 (MQ=60)
GAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCG < SRR3722112.548540/100‑1 (MQ=60)
CATTAATGAGCGCTTTGCCCCCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTAC < SRR3722112.290772/100‑1 (MQ=60)
|
AAAGTGACATTCGTCCGTACGATCCGAATACCCAACGACGGGTTGTGCGCGAACGTTTGCAGGCGCTGGAAATCATTAATGAGCGCTTTGCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTAC > NZ_CP009273/2013662‑2013834
|
| 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: ‑ |
