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 |
|
A3 F1 I1 R1
|
781 |
46.9 |
2231650 |
93.5% |
2086592 |
109.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,475,562 |
(G)6→7 |
coding (126/1815 nt) |
yjgL → |
SopA‑central‑domain‑like hexapeptide repeat protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,475,556 | 1 | . | G | 97.9%
| 162.3
/ ‑4.0
| 48 | coding (120/1815 nt) | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (25/22); total (25/23) |
| Fisher's exact test for biased strand distribution p-value = 4.79e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑GGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTC > NC_000913/4475425‑4475686
|
aaGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑ggggggg > 1:1032637/1‑138 (MQ=255)
aaGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑ggggggg < 1:1096690/139‑2 (MQ=255)
aaGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑ggggggg < 2:928918/139‑2 (MQ=255)
cGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATaa > 1:729418/1‑139 (MQ=255)
gCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGa > 2:572954/1‑139 (MQ=255)
tttAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTcc < 1:666609/139‑1 (MQ=255)
ttCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATaa > 1:1062711/1‑109 (MQ=255)
ttCTCAACACAGTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATaa < 2:1062711/109‑1 (MQ=255)
attacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGttt > 1:976994/1‑139 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑gg < 2:279036/84‑1 (MQ=255)
tacattaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑gg > 1:279036/1‑84 (MQ=255)
attaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATaa > 2:544888/1‑94 (MQ=255)
attaGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATaa < 1:544888/94‑1 (MQ=255)
taGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGa > 2:820776/1‑96 (MQ=255)
taGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGa < 1:820776/96‑1 (MQ=255)
taGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaa > 1:1071126/1‑139 (MQ=255)
aGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaaa < 1:946377/139‑1 (MQ=255)
gCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAg > 1:999237/1‑139 (MQ=255)
gCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑ggggggg < 1:941987/82‑2 (MQ=255)
gCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑ggggggg > 2:941987/1‑81 (MQ=255)
ccGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaa > 1:342331/1‑136 (MQ=255)
ccGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaa < 2:342331/136‑1 (MQ=255)
ccGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaa > 2:149923/1‑136 (MQ=255)
ccGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaa < 1:149923/136‑1 (MQ=255)
ccGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGa > 1:949163/1‑139 (MQ=255)
ccGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑ggggggg > 2:789575/1‑80 (MQ=255)
ccGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑ggggggg < 1:789575/81‑2 (MQ=255)
gACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaaa < 1:84496/135‑1 (MQ=255)
gACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaaa > 2:84496/1‑135 (MQ=255)
gACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATACTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGata > 2:262650/1‑139 (MQ=255)
aaaaGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAg > 2:231780/1‑75 (MQ=255)
aaaaGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAg < 1:231780/75‑1 (MQ=255)
tGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGa > 2:305195/1‑139 (MQ=255)
tAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCa < 2:949163/139‑1 (MQ=255)
tAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCa < 1:262650/139‑1 (MQ=255)
aaaaCCTGGCTTGTTGGAATGAATGATTTTGCCCGTATTGGCG‑GGGGGGCAGGATAACAGAGGGTATATTCTTTCTCCTTGAGCATTTTTAGAGTTTTTGGCAAAGGTATTTACCTTGGGTTATGTGGATTTTAGCaaa < 1:697031/136‑1 (MQ=255)
cTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTc > 1:1054532/1‑139 (MQ=255)
ggCGTGTTGGAATGAATGATTTTGCCCGTATT‑Gcc < 2:1103595/35‑1 (MQ=255)
ggCGTGTTGGAATGAATGATTTTGCCCGTATT‑Gcc > 1:1103595/1‑35 (MQ=255)
ggCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGAt > 1:877064/1‑48 (MQ=255)
ggCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGAt < 2:877064/48‑1 (MQ=39)
tgtTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATAttctt < 2:244575/62‑1 (MQ=255)
tgtTGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATAttctt > 1:244575/1‑62 (MQ=255)
tGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCaaa < 2:162542/125‑1 (MQ=255)
tGGAATGAATGATTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCaaa > 1:162542/1‑125 (MQ=255)
atgaatgaTTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGt < 2:1071126/139‑1 (MQ=255)
atgaTTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGaa > 2:630462/1‑139 (MQ=255)
tgaTTTTGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGaaa > 1:637373/1‑139 (MQ=255)
tttGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAg > 1:274733/1‑56 (MQ=255)
tttGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAg < 2:274733/56‑1 (MQ=255)
tttGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCggg < 2:535764/129‑1 (MQ=255)
tttGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCggg > 1:535764/1‑129 (MQ=255)
tttGCCCGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATatg < 1:305195/139‑1 (MQ=255)
cGTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCt < 1:163932/139‑1 (MQ=255)
gTATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTc < 1:630462/139‑1 (MQ=255)
tATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaaa > 1:325993/1‑70 (MQ=255)
tATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCaaa < 2:325993/70‑1 (MQ=255)
tATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTggg < 2:374286/85‑1 (MQ=255)
tATT‑GCCGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTggg > 1:374286/1‑85 (MQ=255)
|
AAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATT‑GCC‑GGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTC > NC_000913/4475425‑4475686
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
