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 |
|
A5 F19 I1 R1
|
54 |
86.9 |
3694430 |
98.4% |
3635319 |
146.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,423 |
+GCC |
intergenic (‑84/+87) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,423 | 1 | . | G | 87.5%
| 39.5
/ 1.4
| 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base G (9/5); total (9/7) |
| Fisher's exact test for biased strand distribution p-value = 1.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.26e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 87.5%
| 45.4
/ 0.8
| 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (9/5); total (9/7) |
| Fisher's exact test for biased strand distribution p-value = 1.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 87.5%
| 45.5
/ 0.8
| 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (9/5); total (9/7) |
| Fisher's exact test for biased strand distribution p-value = 1.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01 |
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG > NC_002947_CJ‑RC/5558276‑5558550
|||
cGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑gcg < 5:194618/148‑1 (MQ=255)
aGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATCGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTcc < 6:399415/149‑1 (MQ=38)
aGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTcc > 1:423036/1‑149 (MQ=255)
aGGGCGGCCTGGGCAGCTATTCGGGGGGCGTACATGAGCAACTCCTTTTTTCTTGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCGTTGTGTCGCTAATGGGCCGCATC‑‑‑GCGGCCCCGGCAATTTCCGCGTGTAt < 4:206336/148‑1 (MQ=255)
aGGGCGGCCTGGGCAGCTATTAGGCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGAATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTAt < 1:1319/148‑1 (MQ=37)
tGGGCTGCTATTTGTCGGGCGTAAATGAGAAACTCTTTTTGTCATGGGCCGCCTACTGAATAGAAACCCCGCTCTGTTGTGGTAGCGGCGTTGTGTCGCTAATGGGCCGAATAGGGGCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAAcc < 4:202879/149‑1 (MQ=255)
gCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg > 7:245091/1‑148 (MQ=255)
tggggCGGACTTGAGCATCTCTTTTTGTGTTGTGTCGCGTACAGCATAGCAACACCGTTCTGTTGTGGGAGCGGCCTTGTGTCGCGAATGGGCGGATTAGGGGCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATg < 2:423036/146‑1 (MQ=255)
gggCGTACATTACCAACTCCTTTTGTCTTGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCa < 8:245091/148‑1 (MQ=37)
aCATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCCGCAATTTACGCGTGTATGCAACAAACCAGGGGCTGCTATGCAGCCCta > 3:310273/1‑147 (MQ=38)
gCAACTCCTTTTGTCATGTGTCGCCGACGGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGAATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 2:292292/148‑1 (MQ=38)
tagtgtCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 4:105297/3‑149 (MQ=38)
tCGCGCAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTACGCGTGTATGCCACACCCCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGCCCTGGCCACCGCTGGCGCGCAGCTgcgc > 6:255933/1‑149 (MQ=25)
tCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 1:249091/1‑149 (MQ=255)
cgcgAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgcc > 6:60744/1‑149 (MQ=255)
gcgAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 5:123652/1‑149 (MQ=255)
gAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTAGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 7:199455/1‑147 (MQ=255)
|||
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG > NC_002947_CJ‑RC/5558276‑5558550
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
