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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,922,713 |
A→C |
T376P (ACC→CCC) |
sdaC → |
HAAAP family serine/threonine permease SdaC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,922,713 | 0 | A | C | 94.1%
| 47.7
/ ‑3.2
| 17 | T376P (ACC→CCC) | sdaC | HAAAP family serine/threonine permease SdaC |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base C (9/7); total (10/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01 |
AACCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAAACCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAGTA > NZ_CP009273/2922632‑2922795
|
aaCCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGc < 1:375076/90‑1 (MQ=255)
aCCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCg < 2:452373/90‑1 (MQ=255)
aCTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAatc > 2:114336/1‑90 (MQ=255)
gcTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAAACCCTGGGCGGTCCAATCATcgc > 1:285376/1‑90 (MQ=255)
gTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTc > 1:416441/1‑90 (MQ=255)
tGGAGTGTTGCCACCCTGAACCCGAGCATCCTGGCTATAATTGAACCCCTTCGCGGGCCAATCATCGCGATGACACTGTTCCTCACGCCg > 2:175731/1‑90 (MQ=255)
aTTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATg < 1:339772/90‑1 (MQ=255)
tGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGa < 1:364601/90‑1 (MQ=255)
gAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGaa > 2:224960/1‑90 (MQ=255)
gAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGaa < 1:201485/90‑1 (MQ=255)
aaCCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGaaa < 2:304681/90‑1 (MQ=255)
aTGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAg > 2:451486/1‑90 (MQ=255)
tGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAGt > 1:163125/1‑90 (MQ=255)
gATTGCACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGAGGCAGATGAACGCAATTCAGAAAGTCCCGGCAAGGCGTAAGTa > 2:232549/1‑90 (MQ=255)
gATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAGTa > 2:44963/1‑90 (MQ=255)
aTTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGaaa > 1:447504/1‑69 (MQ=255)
aTTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGaaa < 2:447504/69‑1 (MQ=255)
|
AACCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAAACCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAGTA > NZ_CP009273/2922632‑2922795
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 27 ≤ 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
CAACAAGCTGAACCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAAACCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAGTACAGCGGTCACA > NZ_CP009273/2922622‑2922806
|
CAACAAGCTGAACCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGC < SRR3722114.168095/100‑1 (MQ=60)
CAACAAGCTGAACCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGC < SRR3722114.488916/100‑1 (MQ=60)
AACCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCA < SRR3722114.379583/100‑1 (MQ=60)
GTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAAACCCTGGGCGGTCCAATCATCGC > SRR3722114.288379/1‑100 (MQ=60)
GTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTC > SRR3722114.421543/1‑100 (MQ=60)
GACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCctgtctcttatacacatctccgagcccacgagaccgtactag > SRR3722114.269781/1‑58 (MQ=60)
ATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTC < SRR3722114.343610/100‑1 (MQ=60)
TGAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGC < SRR3722114.368909/100‑1 (MQ=60)
GAACCCGAGCATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCA < SRR3722114.203447/100‑1 (MQ=60)
ATCCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAGT > SRR3722114.164747/1‑100 (MQ=60)
CCTGGGTATGATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAActgtctcttat > SRR3722114.453055/1‑89 (MQ=60)
ATTGAACCCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAGTACAGCGGTCACA > SRR3722114.408746/1‑100 (MQ=60)
|
CAACAAGCTGAACCGTATCACTGCGCTGTTCATGCTGGTAACGACCTGGATTGTTGCCACCCTGAACCCGAGCATCCTGGGTATGATTGAAACCCTGGGCGGTCCAATCATCGCGATGATCCTGTTCCTGATGCCGATGTACGCAATTCAGAAAGTACCGGCAATGCGTAAGTACAGCGGTCACA > NZ_CP009273/2922622‑2922806
|
| 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: ‑ |
