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 |
4,108,830 |
A→G |
H143H (CAT→CAC) |
rraA ← |
ribonuclease E activity regulator RraA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,108,830 | 0 | A | G | 94.9%
| 108.7
/ ‑0.8
| 40 | H143H (CAT→CAC) | rraA | ribonuclease E activity regulator RraA |
| Reads supporting (aligned to +/- strand): ref base A (2/0); new base G (24/13); total (27/13) |
| Fisher's exact test for biased strand distribution p-value = 5.44e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.58e-01 |
GAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCG > NZ_CP009273/4108743‑4108912
|
gAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTg > 2:659837/1‑90 (MQ=255)
aaaaGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTc < 1:496332/90‑1 (MQ=255)
ggCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCg < 1:595639/90‑1 (MQ=255)
aCCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGgag > 1:380231/1‑90 (MQ=255)
aCCTTGCGGAGCCTTTCTTATCATTCAATATCCAGCGGATGTTCTGAAAGAATAATCCCGGGATTGTGGGCATAAAGCGCGACGCCGgag > 1:1200552/1‑90 (MQ=255)
cTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGagaa > 1:602316/1‑90 (MQ=255)
ttGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGagaag < 2:876827/90‑1 (MQ=255)
ttGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGagaag < 2:1368832/90‑1 (MQ=255)
gCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGa > 2:71628/1‑90 (MQ=255)
gCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAACGTGGTCGCCGGAGAAGAAGGTGa > 2:264094/1‑90 (MQ=255)
ttCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGGCGCCGGAGAAGAAGGTGACAcc > 2:1287727/1‑90 (MQ=255)
tCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCaaa > 1:542571/1‑90 (MQ=255)
cATTCAGTATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCaaaa > 1:550818/1‑90 (MQ=255)
aaTATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGAc > 2:1402714/1‑90 (MQ=255)
tCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCgg < 2:647136/90‑1 (MQ=255)
cAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGAc > 1:1486600/1‑90 (MQ=255)
aGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACa < 2:1484560/90‑1 (MQ=255)
aGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACa > 1:630925/1‑90 (MQ=255)
gCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACAt < 2:1135965/90‑1 (MQ=255)
gCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGGGGTCGCCGGAGAAGAAGGTGACCCCGCCAAAATTGACGCGGACAt < 1:1565546/90‑1 (MQ=255)
gATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGc > 2:304414/1‑90 (MQ=255)
tcttctGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCtt > 1:837907/1‑90 (MQ=255)
tctGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCg > 2:1436208/1‑90 (MQ=255)
tGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGGCATCGCTTTCGcc > 2:341646/1‑90 (MQ=255)
tGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGcc > 1:109567/1‑90 (MQ=255)
aaaGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCaa < 1:1249962/90‑1 (MQ=255)
ggTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGc > 1:1018151/1‑90 (MQ=255)
ggTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGc > 2:1556744/1‑90 (MQ=255)
ggTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGc < 1:3115/90‑1 (MQ=255)
ttGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCa > 1:553020/1‑90 (MQ=255)
tGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAc > 2:783771/1‑90 (MQ=255)
tGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAc < 1:364/90‑1 (MQ=255)
tGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAc > 2:1438724/1‑90 (MQ=255)
gTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAcc > 2:1026776/1‑90 (MQ=255)
gTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAcc > 1:1020155/1‑90 (MQ=255)
gTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAcc > 1:819842/1‑90 (MQ=255)
ggCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAAc > 2:636153/1‑90 (MQ=255)
gCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAAcc < 1:333648/90‑1 (MQ=255)
gCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAAcc < 2:1050944/90‑1 (MQ=255)
cATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCg > 1:187733/1‑90 (MQ=255)
|
GAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCG > NZ_CP009273/4108743‑4108912
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ 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
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCGCCATC > NZ_CP009273/4108731‑4108926
|
gtcagatgtgtataagagacagACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722078.419499/78‑1 (MQ=60)
cagcgtcagatgtgtataagagacagTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722078.1246993/74‑1 (MQ=60)
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722078.998637/100‑1 (MQ=60)
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722078.1043612/100‑1 (MQ=60)
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722078.1576473/100‑1 (MQ=60)
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722078.1264335/100‑1 (MQ=60)
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722078.1538771/100‑1 (MQ=60)
CGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCC < SRR3722078.254251/100‑1 (MQ=60)
GAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAG > SRR3722078.384872/1‑100 (MQ=60)
AAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAA > SRR3722078.609274/1‑100 (MQ=60)
AAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAG < SRR3722078.502209/100‑1 (MQ=60)
GGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGG < SRR3722078.602545/100‑1 (MQ=60)
GCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAA > SRR3722078.548979/1‑100 (MQ=60)
CCTTTCTTATCATTCAGTATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAA > SRR3722078.557321/1‑100 (MQ=60)
ATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGAC > SRR3722078.1510836/1‑100 (MQ=60)
TTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACA > SRR3722078.638183/1‑100 (MQ=60)
ATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTT > SRR3722078.849058/1‑100 (MQ=60)
GCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCC > SRR3722078.110860/1‑100 (MQ=60)
GCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGGGGTCGCCGGAGAAGAAGGTGACCCCGCCAAAATTGACGCGGACATCGCTTTCGCC < SRR3722078.1591036/100‑1 (MQ=60)
AAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCC < SRR3722078.1269747/100‑1 (MQ=60)
GAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGC > SRR3722078.1033183/1‑100 (MQ=60)
AATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCA > SRR3722078.559544/1‑100 (MQ=60)
TCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACC > SRR3722078.830689/1‑100 (MQ=60)
TCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACC > SRR3722078.1035239/1‑100 (MQ=60)
GGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACC < SRR3722078.3144/100‑1 (MQ=60)
GTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCG > SRR3722078.189959/1‑100 (MQ=60)
TGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAAT < SRR3722078.369/100‑1 (MQ=60)
GTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATT > SRR3722078.1427544/1‑100 (MQ=60)
GCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACTCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCG > SRR3722078.534223/1‑100 (MQ=60)
GCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTgtctcttatacacatctgacgctgccga > SRR3722078.781949/1‑72 (MQ=60)
GCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCG < SRR3722078.337725/100‑1 (MQ=60)
GCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCG > SRR3722078.1412153/1‑100 (MQ=60)
GCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCG > SRR3722078.1242410/1‑100 (MQ=60)
AAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCctgtctcttatacacatctgacgctgcc > SRR3722078.1003904/1‑72 (MQ=60)
|
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCGCCATC > NZ_CP009273/4108731‑4108926
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
