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
A17 F109 I0 R1 32 27.2 584098 96.5% 563654 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,481,355 G→T 100% A6890E (GCA→GAA)  ebh ← extracellular matrix binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,481,3550GT96.2% 69.8 / ‑5.9 28A6890E (GCA→GAA) ebhextracellular matrix binding protein
Reads supporting (aligned to +/- strand):  ref base G (2/0);  new base T (9/17);  total (11/17)
Fisher's exact test for biased strand distribution p-value = 1.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCTGTATTCAGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTGCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATATTTTCAGCAGC  >  CP000730/1481223‑1481491
                                                                                                                                    |                                                                                                                                        
gCTGTATTCAGTTCCTGGTCGGTTTGAATGTCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGtt                                                                                                                                   <  2:190014/140‑1 (MQ=255)
      ttCAGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTAAAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACGTTTTTGTGCATTGTTTAAGTTATCTCACGTGGATAATGTTTGGTTTTCGTTGTTTTTAga                                                                                                                             >  2:91911/1‑139 (MQ=255)
                          aaTGTCTTGCGTTATGTCCGCTACCGTGTGTGCTTGATTGATGTTTCCAGTAACAGCACTTTTTTGTGCATTGTTTAACTTATCTATCCTAGATAAGGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCat                                                                                                         <  2:32071/140‑2 (MQ=255)
                              gCTTGCGTTACTTCAGCTAAAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCAACTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCTTCTGTTACTTTTCTATCACCAtt                                                                                                     >  1:188798/1‑140 (MQ=255)
                                  gCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCacc                                                                                                 >  2:229755/1‑138 (MQ=255)
                                   gtttACTTCAGTGACAGTGTGCGCTTGATTGATGTTTTCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACg                                                                                                <  2:153428/138‑1 (MQ=255)
                                                 cAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAgtt                                                                                  <  1:191065/140‑1 (MQ=255)
                                                   gtgtGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGCGCATTGTTTAAGATATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCCTGTTTCGTAgttgt                                                                                >  2:245856/1‑140 (MQ=255)
                                                                           gTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTTCTGCTTCAAc                                                        <  2:196565/140‑1 (MQ=255)
                                                                            tAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACt                                                       <  2:278050/140‑1 (MQ=255)
                                                                                  taCCTTTTTGTGTTTTGTTTAACTTTTCTAACGTAGATAATTTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCCATTCTCGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGAt                                                 <  1:127647/139‑1 (MQ=255)
                                                                                     cTTTTTTTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTgg                                              <  2:230994/140‑1 (MQ=255)
                                                                                         ttGTGCATTGTTTAAGTTATCTAACGTAGATTATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCg                                          <  1:175310/140‑1 (MQ=255)
                                                                                         ttGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCg                                          <  2:267621/140‑1 (MQ=255)
                                                                                               aTTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTg                                    <  1:31051/140‑1 (MQ=255)
                                                                                                  gTTTAAGTTATCTAACGTATATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTAc                                 <  1:60849/140‑1 (MQ=255)
                                                                                                      aaGTTATCTAACGTAGATAATGTTTTGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCAtt                             <  1:209502/140‑1 (MQ=255)
                                                                                                         ttATCTATCGTAGATAATGTTTGTTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGc                          <  2:55586/140‑1 (MQ=255)
                                                                                                           aacTAACATAGATACTGTTTGGATTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCCACTCACGGTTGGTTCGCATTTGTACCATTTGCtt                        >  2:60293/3‑140 (MQ=255)
                                                                                                           aTCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTTAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTTTGCTTGGTTGGAATTTGTTACATTTGCtt                        >  2:180909/1‑140 (MQ=255)
                                                                                                             cTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGa                      >  2:47793/1‑140 (MQ=255)
                                                                                                               aaCGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGAtt                    >  1:105474/1‑140 (MQ=255)
                                                                                                               aaCGGAGATAATGATTGGTTTGCAGTGTTATGAGCATCGGTTACTTGTCTATCACCATTCAACGCTGGGTTCGTAGTACAGGCAGTGGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGGACCATTTGCTTGAtt                    >  2:73097/1‑140 (MQ=255)
                                                                                                                aCGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTCCAGTTGTAAGTGCTGCTTCAACTTGTGATTGGTTCGCGTTTGTAACATTTGCTGGATta                   >  1:105242/1‑140 (MQ=255)
                                                                                                                  gTAGATAAAGTTTGGTTTGCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTCGATaaat                 >  2:172982/1‑140 (MQ=255)
                                                                                                                    aGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATtaataa               <  1:263069/140‑1 (MQ=255)
                                                                                                                        aaTTTTTGGTTTTCATTGGTTTTAGCCTCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAATTTGTGATTTGTTCGCATTTGTACCATTTGCTTGATTAATAATAtt           <  2:48870/140‑1 (MQ=255)
                                                                                                                         aTGTTTGGTTTTCATTGTTTTTAGCACCTGTTAATTTTTTATCTCCATTCTACGCTTGTATGGTCGTTGTGAGAGTAGACAGTGAACGTAAAACTTTTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATAttt          <  1:139621/140‑1 (MQ=255)
                                                                                                                              tggttttCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATATTTTcagc     >  2:235378/1‑140 (MQ=255)
                                                                                                                                 ttttCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATATTTTcagaagc  >  2:41948/1‑140 (MQ=255)
                                                                                                                                    |                                                                                                                                        
GCTGTATTCAGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTGCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATATTTTCAGCAGC  >  CP000730/1481223‑1481491

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A