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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,706,273 |
T→C |
S7P (TCC→CCC) |
srmB → |
ATP‑dependent RNA helicase SrmB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,706,273 | 0 | T | C | 95.0%
| 56.4
/ ‑6.2
| 20 | S7P (TCC→CCC) | srmB | ATP‑dependent RNA helicase SrmB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (13/6); minor base A (0/1); total (13/7) |
| Fisher's exact test for biased strand distribution p-value = 3.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TACAAACAGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTTCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCTGC > NZ_CP009273/2706193‑2706352
|
tACAAACAGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTg > 1:276484/1‑90 (MQ=255)
aaCAGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACt > 2:64077/1‑90 (MQ=255)
aGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTcga > 2:229375/1‑90 (MQ=255)
aTTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGcc < 2:276484/90‑1 (MQ=255)
ttGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCct > 2:121575/1‑90 (MQ=255)
tAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGc < 2:431960/90‑1 (MQ=255)
tAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGc < 2:368525/90‑1 (MQ=255)
tAACGTCTATAATCAGCGCCCCAAACAGAGGTAGAACATGACTGTACCGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGc < 2:341910/90‑1 (MQ=255)
aCGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGccc < 1:266401/90‑1 (MQ=255)
tCTATAATCAGCGCCCCACACAAAGGTACACCATGCCGGCACCGGCTTTTACCGAAATTGAACCCGACGAAAGCCTGCTGGACGCCCTcc < 2:218495/90‑1 (MQ=255)
cAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTTGACGAAAGCCTGCTGGAAGCCCTCCAGGATaaa > 2:113076/1‑90 (MQ=255)
cAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATaaa > 1:176218/1‑90 (MQ=255)
aGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAg > 2:145289/1‑90 (MQ=255)
tAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGAcc < 1:139359/90‑1 (MQ=255)
aGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCg > 2:53309/1‑90 (MQ=255)
gACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCa > 2:324001/1‑90 (MQ=255)
gACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCAGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCa > 2:367002/1‑90 (MQ=255)
gTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCt > 1:11842/1‑90 (MQ=255)
gTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCt > 2:48044/1‑90 (MQ=255)
aaCGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCTgc > 1:391895/1‑90 (MQ=255)
|
TACAAACAGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTTCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCTGC > NZ_CP009273/2706193‑2706352
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 28 ≤ 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
CCCGAGAAGCGATATCCATACAAACAGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTTCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCTGC > NZ_CP009273/2706175‑2706352
|
CCCGAGAAGCGATATCCATACAAACAGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCC > SRR3722113.436540/1‑100 (MQ=60)
GCGATATCCATACAAACAGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTG > SRR3722113.278922/1‑100 (MQ=60)
ACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAA < SRR3722113.268749/100‑1 (MQ=60)
CGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAA > SRR3722113.177619/1‑100 (MQ=60)
TAGAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGG < SRR3722113.140522/100‑1 (MQ=60)
GAACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCT > SRR3722113.11948/1‑100 (MQ=60)
ACATGACTGTAACGACTTTTCCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCTGC > SRR3722113.396000/1‑100 (MQ=60)
|
CCCGAGAAGCGATATCCATACAAACAGATGAAGATTGCAGCCGTAACGTCTATAATCAGCGCCCCACACAGAGGTAGAACATGACTGTAACGACTTTTTCCGAACTTGAACTCGACGAAAGCCTGCTGGAAGCCCTCCAGGATAAAGGTTTCACTCGCCCGACCGCCATTCAGGCTGC > NZ_CP009273/2706175‑2706352
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
