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
A0 F0 I1 R1 715 38.4 1606192 96.6% 1551581 120.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,450,392 C→T A320T (GCA→ACA)  tynA ← tyramine oxidase, copper‑requiring

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,450,3920CT94.4% 49.1 / ‑6.1 18A320T (GCA→ACA) tynAtyramine oxidase, copper‑requiring
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (9/8);  minor base A (1/0);  total (10/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGTTCCGCCAGTGAATCATATCGCCAGTAATGGTGTAATTTTTACCTTCAGGCTCAATGATTTGCATAGGCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGCGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGCCACCAGGTTTTCGATGGGATGTGCCC  >  NC_000913/1450277‑1450490
                                                                                                                   |                                                                                                  
cAGTTCCGCCAGTGAATCATATCGCCAGTAATGGTGTAATTTTTACCTTCAGGCTCAATGATTTGCATAGGCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCg                                                                             >  2:792581/1‑139 (MQ=255)
       gCCAGTGAATCATATCGCCAGTAATAGTGTCATCTTTACCTCCAGGCGCAATGCCTTGGCTAGGCTCCACTGCCGGAGCAACACGGTCAGGGCCCTCAAAAGGGCGAGTGGTCGTTGGCACCGGAACTACCGGGCctta                                                                      >  1:269120/1‑138 (MQ=255)
                   tatCGCCAGTAATGGTGTAATTTTTACCTTCAGGCTCAATGATTTGCATAGGCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAAc                                                          >  2:721311/1‑139 (MQ=255)
                            tAATGGTGTAATTTTTACCTTCAGGCTCAATGATTTGCATAGGCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGAttttttt                                                 >  1:417531/1‑139 (MQ=255)
                                  tgtAATTTTTACCTTCAGGCTCAATGATTTGCATAGGCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTc                                           >  2:728505/1‑139 (MQ=255)
                                                     cTCAATGATTTGCATAGGCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGccacc                        <  2:526394/139‑1 (MQ=255)
                                                                gCATAGGCTTAACTGCCGGAGTAACGCGTTCACGGCCATCAGATGGGCGTGTGGTCATTGGCAACGGAACTACCGGACCTTCTTCTAGCTTAACGATTTTTTTCTGTTGTAAATCAACGACCGCCACCAGGTTTTCGAt             <  1:724734/139‑1 (MQ=255)
                                                                gCATAGGCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGCCACCAGGTTTTCGAt             <  2:799919/139‑1 (MQ=255)
                                                                      gCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGCCACCAGGTTTTCGATGGGAtg       <  2:417531/139‑1 (MQ=255)
                                                                      gCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGCCACCAGGTTTTCGATGGGAtg       >  1:390067/1‑139 (MQ=255)
                                                                           aCTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCgg                                                                                     >  2:117721/1‑56 (MQ=255)
                                                                           aCTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCgg                                                                                     <  1:117721/56‑1 (MQ=255)
                                                                           aCTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGCCACCAGGTTTTCGATGGGATGTGacc  >  2:422046/1‑139 (MQ=255)
                                                                                cGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCAc                                                                                        <  2:336154/48‑1 (MQ=255)
                                                                                cGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCAc                                                                                        >  1:336154/1‑48 (MQ=255)
                                                                                cGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGCCACCAGGTTTTCGATGGGAt        >  1:734442/1‑128 (MQ=255)
                                                                                cGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGCCACCAGGTTTTCGATGGGAt        <  2:734442/128‑1 (MQ=255)
                                                                                                            gggCGTGTGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCtt                                                             <  2:524654/47‑1 (MQ=255)
                                                                                                            gggCGTGAGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCtt                                                             >  1:524654/1‑47 (MQ=255)
                                                                                                                   |                                                                                                  
CAGTTCCGCCAGTGAATCATATCGCCAGTAATGGTGTAATTTTTACCTTCAGGCTCAATGATTTGCATAGGCTTAACTGCCGGAGCAACGCGGTCACGGCCATCAAATGGGCGTGCGGTCATTGGCACCGGAACTACCGGACCTTCTTCAATCTTAACGATTTTTTTCTGTTCTAAATCAACGACCGCCACCAGGTTTTCGATGGGATGTGCCC  >  NC_000913/1450277‑1450490

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A