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 |
|
A9 F200 I1 R1
|
100 |
75.0 |
3643689 |
96.7% |
3523447 |
99.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,595,315 |
(A)5→4 |
coding (166/1278 nt) |
livM ← |
branched‑chain amino acid ABC transporter permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,595,311 | 0 | A | . | 94.9%
| 238.4
/ 9.9
| 60 | coding (170/1278 nt) | livM | branched‑chain amino acid ABC transporter permease |
| Reads supporting (aligned to +/- strand): ref base A (3/0); new base . (27/29); total (31/29) |
| Fisher's exact test for biased strand distribution p-value = 2.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.03e-01 |
TTCTGCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGAAAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCTCCAGTTGCA > NC_000913/3595212‑3595404
|
ttCTGCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGgaaga > 2:1122492/1‑100 (MQ=255)
tCTGCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGgaagaa > 1:578602/1‑100 (MQ=255)
tCTGCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGgaagaa > 1:578608/1‑100 (MQ=255)
tGCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGaaaa < 1:1271022/100‑1 (MQ=255)
gCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGaaaag > 2:727852/1‑99 (MQ=255)
gCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGaaaag < 1:33603/100‑2 (MQ=255)
gCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGaaaag < 1:396978/100‑2 (MQ=255)
ttCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGaaaagac > 2:1473984/1‑97 (MQ=255)
ttCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGaaaagac < 2:150126/100‑4 (MQ=255)
ttCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGAAAAAGa > 2:1094348/1‑100 (MQ=255)
ttCACCGTGGAGCCATCAATGGCGGGCAGAATAAAATTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGaaaagac > 1:565969/1‑97 (MQ=255)
cacccgggAGACAGCAATGGCGGGCACCATAACCTTCTGTCCGTAAATGCTTTTCAACCCTTTCTGCAAAGCCGGTCGCAATAGCTGGAAGaaaaga < 1:755931/91‑3 (MQ=255)
cACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGacca > 2:1219831/1‑100 (MQ=255)
cGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCAccg > 1:1798915/1‑100 (MQ=255)
tGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCAccgcc < 1:741058/100‑1 (MQ=255)
cATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCg > 1:128993/1‑100 (MQ=255)
cATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAACTGGAAG‑AAAAGACCACCGCCGTGCCg > 2:585143/1‑100 (MQ=255)
aTCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGa > 1:1168413/1‑100 (MQ=255)
cAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGAt < 1:1493752/99‑1 (MQ=255)
aaTGGCGGGCAGAATAAACTTCTGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGAt < 1:1701822/98‑1 (MQ=255)
ggCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAaca > 2:1651727/1‑100 (MQ=255)
ggCGGGCAGAATAAACCTCAGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGACGGTCGAAAAAGCTGGAAG‑AAAAGACCACCGACATGACGATAAaca > 1:825010/1‑100 (MQ=255)
ggtcataaTAAACATGGGGCGGGTAAGGCGTTCTAACCCTTTCTGGAAACCCGGTAGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATCAac < 1:653534/90‑1 (MQ=255)
gggCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACAccc > 1:1551855/1‑100 (MQ=255)
cAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACt > 2:166598/1‑100 (MQ=255)
aGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAATAGCTGGAAG‑ACAAGACCACCGCCGTGCCGATAAACACCCACt < 2:1224843/99‑1 (MQ=255)
aTAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTTCCGATAAACACCCACTGCCa < 1:1779387/100‑1 (MQ=255)
aaCTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACg > 2:1404896/1‑100 (MQ=255)
aaCTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACg < 2:1551866/100‑1 (MQ=255)
aaCTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACg < 2:905963/100‑1 (MQ=255)
aaCTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAACTGGAAGAAAAA‑ACAACCACAGTGCCAAAAAAAACCCACTGCCAACg > 2:89381/1‑100 (MQ=255)
ggTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCTATAAACACCCACTGCCAACGGACATc < 1:40442/100‑1 (MQ=255)
gTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATcc < 2:1802818/100‑1 (MQ=255)
gTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATcc < 2:128993/100‑1 (MQ=255)
ggAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTTGAAG‑AAAACACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGaa > 2:345598/1‑99 (MQ=255)
ggAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGAAAAACACCACCGCCGTGCCGATAAACACCCACTGCAAACGGACATCCGaa > 1:151399/1‑100 (MQ=255)
gAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGc < 1:467574/100‑1 (MQ=255)
gAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGc < 1:1255603/100‑1 (MQ=255)
gAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGc < 1:1480895/100‑1 (MQ=255)
gAAACGCTCTTTAAGCCTTTCTGTAGAGTCGGCCGCAAAAGCTGGAAG‑AATAGGCCACCGCCGTGCCGATAAACACTCTCTGCCAACGGACATCCGAAGc < 1:19413/100‑1 (MQ=255)
aaCGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCGCTGCCAACGGACATCCGAAGCCg > 1:1411413/1‑100 (MQ=255)
aaCGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCg < 1:1638922/100‑1 (MQ=255)
aaCGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCg < 2:1785332/100‑1 (MQ=255)
cGCTTTTCAACCCTTTCTGGAAAGTCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCgt > 1:1238238/1‑99 (MQ=255)
cGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCgtg > 1:490562/1‑100 (MQ=255)
cGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCgtg < 1:330586/100‑1 (MQ=255)
cTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTc > 2:1588721/1‑100 (MQ=255)
cTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTc < 2:1386591/100‑1 (MQ=255)
ttttCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCg < 1:1571636/100‑1 (MQ=255)
ttttCAACCCTTTCTGGAAAGCCGGTAGCAAAAGCTGGAA‑CAAAAGACCACCGCCGTGCCGATAAACACCAACAGCCAAAGGACAGCCGAAAACGTGTCg > 1:1666075/1‑100 (MQ=255)
tttCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGa < 2:490565/100‑1 (MQ=255)
tttCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGa > 2:1695432/1‑100 (MQ=255)
ttCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGac < 2:104738/100‑1 (MQ=255)
cAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGacca > 2:1119777/1‑100 (MQ=255)
cAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGacca > 1:1282698/1‑100 (MQ=255)
ccTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAGCACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAg > 1:1279193/1‑100 (MQ=255)
ggAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTg > 2:1163930/1‑100 (MQ=255)
ggAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTg > 1:362831/1‑100 (MQ=255)
gAAAGCCGGTCGCAACAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTtgctgc > 1:1428918/1‑100 (MQ=255)
gAAAGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTg < 2:1300130/99‑1 (MQ=255)
aaccGGTCGCAAAGGCTGGAAG‑AAAAGACCAACGCCGTGCCGTTAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCAt > 2:1226195/3‑100 (MQ=255)
aGCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCAt < 2:1485711/100‑1 (MQ=255)
gCCGGTCGCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATc < 2:701457/100‑1 (MQ=255)
gCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCt < 1:1541810/98‑1 (MQ=255)
gCAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCTcc < 2:1032487/100‑1 (MQ=255)
cAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCTCCa > 2:727581/1‑100 (MQ=255)
cAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGAAATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCTCCa > 1:750772/1‑100 (MQ=255)
cAAAAGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACAACCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCTCCa > 1:1403582/1‑100 (MQ=255)
aaaaGCTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCTCCAg < 1:1624744/100‑1 (MQ=255)
cTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCTCCAGTTGCa < 1:1317692/100‑1 (MQ=255)
cTGGAAG‑AAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCCCCAGTTGCa > 1:887118/1‑100 (MQ=255)
|
TTCTGCTTCACCGTGGAGCCATCAATGGCGGGCAGAATAAACTTCGGTCCGGAAACGCTTTTCAACCCTTTCTGGAAAGCCGGTCGCAAAAGCTGGAAGAAAAAGACCACCGCCGTGCCGATAAACACCCACTGCCAACGGACATCCGAAGCCGTGTCGACCACCAGTTTGGTGCCATCCAGCTCCAGTTGCA > NC_000913/3595212‑3595404
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
