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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
951,809 |
T→G |
T94P (ACC→CCC) |
ycaO ← |
30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 951,809 | 0 | T | G | 97.1%
| 111.1
/ ‑3.7
| 35 | T94P (ACC→CCC) | ycaO | 30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (10/24); total (10/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.50e-01 |
GCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGC > NZ_CP009273/951725‑951890
|
gcagcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGc > 2:464071/1‑90 (MQ=255)
gcagcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGc > 2:1151178/1‑90 (MQ=255)
cagcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGcc < 1:906177/90‑1 (MQ=255)
cagcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGcc < 2:521772/90‑1 (MQ=255)
cagcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGcc < 2:65296/90‑1 (MQ=255)
cagcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGcc < 1:640723/90‑1 (MQ=255)
agcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGccc > 2:285372/1‑90 (MQ=255)
tCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCa > 1:347270/1‑90 (MQ=255)
cATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCaaaaa > 1:996700/1‑90 (MQ=255)
ttCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAagta < 2:1074908/90‑1 (MQ=255)
cGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAagtagt < 1:806258/90‑1 (MQ=255)
ggTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 1:585441/90‑1 (MQ=255)
ggTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 1:380476/90‑1 (MQ=255)
ggTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 1:221701/90‑1 (MQ=255)
ggTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 2:671807/90‑1 (MQ=255)
gAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTgagag < 1:214209/90‑1 (MQ=255)
gAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTgagag < 1:1542807/90‑1 (MQ=255)
ccATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACg < 1:1093154/90‑1 (MQ=255)
aTTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCt > 1:351790/1‑90 (MQ=255)
ttttCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCg < 2:385813/90‑1 (MQ=255)
ttttCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCg < 2:768518/90‑1 (MQ=255)
ttCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGaa < 2:614948/90‑1 (MQ=255)
cGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAat < 1:1164134/90‑1 (MQ=255)
tAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCg < 1:337021/90‑1 (MQ=255)
tAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCg < 2:1550988/90‑1 (MQ=255)
aCGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCa > 1:772308/1‑90 (MQ=255)
cGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAg < 1:1085648/90‑1 (MQ=255)
cGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAg < 1:196871/90‑1 (MQ=255)
ggACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 2:1476080/50‑1 (MQ=255)
ggACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt > 1:1476080/1‑50 (MQ=255)
gTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAg > 1:993617/1‑80 (MQ=255)
gTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAg < 2:993617/80‑1 (MQ=255)
gTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAgcgc > 2:503516/1‑90 (MQ=255)
ggCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGcgccgc < 2:518914/90‑1 (MQ=255)
tGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGaa < 1:1022701/55‑1 (MQ=255)
|
GCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGC > NZ_CP009273/951725‑951890
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTGGTTG > NZ_CP009273/951717‑951901
|
GTCATCGAGTAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCC < SRR3722078.959775/100‑1 (MQ=60)
GTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCC < SRR3722078.450353/100‑1 (MQ=60)
CAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAG < SRR3722078.918363/100‑1 (MQ=60)
CAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAG < SRR3722078.648094/100‑1 (MQ=60)
agccgttgggggaaattgttATTTTCTGTCGGTGGAAACCATTTTTCGTGGGGATAATGCACAAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGT < SRR3722078.1410494/80‑1 (MQ=60)
TTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCA > SRR3722078.351525/1‑100 (MQ=60)
GGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAA > SRR3722078.1011211/1‑100 (MQ=60)
CGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAG < SRR3722078.816902/100‑1 (MQ=60)
GGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA < SRR3722078.224391/100‑1 (MQ=60)
GGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA < SRR3722078.592261/100‑1 (MQ=60)
GGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA < SRR3722078.385122/100‑1 (MQ=60)
AGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCT > SRR3722078.356091/1‑100 (MQ=60)
GAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAA < SRR3722078.216799/100‑1 (MQ=60)
GAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAA < SRR3722078.1567961/100‑1 (MQ=60)
CCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATAT < SRR3722078.1109762/100‑1 (MQ=60)
agcgtcagatgtgtataagagacagCCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCG < SRR3722078.1037848/75‑1 (MQ=60)
CGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAG < SRR3722078.1182201/100‑1 (MQ=60)
GGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCA > SRR3722078.782276/1‑100 (MQ=60)
TAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAG < SRR3722078.341141/100‑1 (MQ=60)
ATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACtgtctcttatacacatctgacgctgccga > SRR3722078.1500159/1‑71 (MQ=60)
CGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGC < SRR3722078.199222/100‑1 (MQ=60)
CGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGC > SRR3722078.1008066/1‑100 (MQ=60)
CGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGC < SRR3722078.1102093/100‑1 (MQ=60)
GTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTG > SRR3722078.1436458/1‑100 (MQ=60)
GTTGGCGATGGGTTCGCCCAGCCAGAAGGCCGCAAAAAAGGAGTTGGTTGAGAGACGCTCGGAATATTCACCGAGGGCAGAAGCCAGCGCCGCTTTCTTG > SRR3722078.984703/1‑100 (MQ=60)
GCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTGGTTG > SRR3722078.1043750/1‑100 (MQ=60)
|
GTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTGGTTG > NZ_CP009273/951717‑951901
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
