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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,486,885 |
A→C |
Q320P (CAG→CCG) |
tsgA → |
MFS transporter TsgA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,486,885 | 0 | A | C | 93.8%
| 45.9
/ ‑3.5
| 16 | Q320P (CAG→CCG) | tsgA | MFS transporter TsgA |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (7/8); total (7/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
TGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTTG > NZ_CP009273/3486813‑3486962
|
tGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGt > 2:252268/1‑90 (MQ=255)
cGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGc > 1:331975/1‑90 (MQ=255)
gTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCaaa < 1:49933/90‑1 (MQ=255)
ctcGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGtt < 1:252268/90‑1 (MQ=255)
ccAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCg > 1:131650/1‑90 (MQ=255)
ccAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCg > 1:236669/1‑90 (MQ=255)
gcgcGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGaa < 1:282941/90‑1 (MQ=255)
aTCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc < 1:308044/90‑1 (MQ=255)
aTCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc < 1:389518/90‑1 (MQ=255)
aTCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc < 2:17776/90‑1 (MQ=255)
aTCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc > 2:70957/1‑90 (MQ=255)
cTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCgg < 2:242455/90‑1 (MQ=255)
taCCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTAc < 1:346912/90‑1 (MQ=255)
atcatcACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc > 1:235646/1‑78 (MQ=255)
atcatcACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc < 2:235646/78‑1 (MQ=255)
cccTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTtg > 1:142088/1‑90 (MQ=255)
|
TGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTTG > NZ_CP009273/3486813‑3486962
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ 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
GCACATATGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTTGTGGTTACCGGCCCGAT > NZ_CP009273/3486806‑3486978
|
GCACATATGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGC > SRR3722094.337402/1‑100 (MQ=60)
GTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAAC < SRR3722094.50629/100‑1 (MQ=60)
CTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCC < SRR3722094.255964/100‑1 (MQ=60)
GGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCG > SRR3722094.133545/1‑100 (MQ=60)
GGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCG > SRR3722094.240021/1‑100 (MQ=60)
GCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTAC < SRR3722094.287193/100‑1 (MQ=60)
ATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGT < SRR3722094.312843/100‑1 (MQ=60)
ATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGT < SRR3722094.396208/100‑1 (MQ=60)
CTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTct > SRR3722094.238967/1‑98 (MQ=60)
TACCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACC < SRR3722094.352665/100‑1 (MQ=60)
ACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTTG > SRR3722094.144092/1‑100 (MQ=60)
GTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTTGTGGTTACCGGCCCGAT > SRR3722094.26698/1‑100 (MQ=60)
|
GCACATATGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTTGTGGTTACCGGCCCGAT > NZ_CP009273/3486806‑3486978
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
