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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	486,641	T→C	S36P (TCA→CCA)	mscK →	mechanosensitive channel protein, intermediate conductance, K+ regulated

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	486,641	0	T	C	96.5%	93.2 / ‑5.6	29	S36P (TCA→CCA)	mscK	mechanosensitive channel protein, intermediate conductance, K+ regulated
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (15/13); total (16/13)
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

TCTTCAGGTTCAGAAACCTTCATTCATCATGACTATGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGTCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAGGATCTGACAGA  >  NC_000913/486508‑486753

tcttcAGGTTCAGAAACCTTCATTCATCATGACTATGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCg                                                                                                             >  1:523057/1‑139 (MQ=255)

          cAGAAACCTTCATTCATCATGACTATGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATc                                                                                                   >  1:152489/1‑139 (MQ=255)

                 cTTCATTCATCATGACTATGTTCCAGTATTACGAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGAc                                                                                            >  2:551730/1‑139 (MQ=255)

                  ttcattcaTCATGACTATGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGAt                                                                                                    >  1:122518/1‑130 (MQ=255)

                  ttcattcaTCATGACTATGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGAt                                                                                                    <  2:122518/130‑1 (MQ=255)

                  ttcattcaTCATGACTATGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTCTTTTTGTCTTGTTATGCCAGAACACGCCGTTTGCTCCGCGGTCACCGAATGGTGATCTGCCGCCa                                                                                           >  2:61819/1‑139 (MQ=255)

                              gACTATGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTg                                                                               >  1:637419/1‑139 (MQ=255)

                                  aTGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAgg                                                                           <  1:510239/139‑1 (MQ=255)

                                    gTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGgcg                                                                         <  1:891356/139‑1 (MQ=255)

                                     ttCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGgcgc                                                                        >  1:424648/1‑139 (MQ=255)

                                        cAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTg                                                                               >  2:269580/1‑129 (MQ=255)

                                        cAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTg                                                                               <  1:269580/129‑1 (MQ=255)

                                            aTTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGa                                                                 <  2:523057/139‑1 (MQ=255)

                                               aCAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTc                                                              >  1:108165/1‑139 (MQ=255)

                                                     gATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACtaaa                                                        >  2:236107/1‑139 (MQ=255)

                                                     gATCACAGCATTTTGTTTTTTCAGCCTGTATTGCTTTTGTTTTTGTCGTGTTATGCCAGAACACGGCGTTTCCGCGGGCGCCATCGAATGGTGATCTGCCGACATACGGGGGCATGCAGGCGCAACTTGACTTACgaaa                                                        >  2:370179/1‑139 (MQ=255)

                                                        cACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACtaaataa                                                     >  2:534990/1‑139 (MQ=255)

                                                                      ttttCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCttt                                       <  2:108165/139‑1 (MQ=255)

                                                                                          tgtttttgtCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTg                   >  1:199303/1‑139 (MQ=255)

                                                                                                 gtCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGCGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTTACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAgg            <  2:339141/139‑1 (MQ=255)

                                                                                                   cTTGTTATGCCTGAACACGGCGTTTTCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAGGAt          <  1:601665/139‑1 (MQ=255)

                                                                                                      gTTATGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAGGATCTg       >  2:632026/1‑139 (MQ=255)

                                                                                                          tGCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAGGATCTGACAg   <  1:236107/139‑1 (MQ=255)

                                                                                                          tGCCAGAACACGGCGTATGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACAGGTGCAGCAGGATCTGTCAg   <  1:632026/139‑1 (MQ=255)

                                                                                                           gCCAGAACACGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAGGATCTGACAGa  <  2:199303/139‑1 (MQ=255)

                                                                                                                    cGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTc                                                              >  2:414754/1‑70 (MQ=255)

                                                                                                                    cGGCGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTc                                                              <  1:414754/70‑1 (MQ=255)

                                                                                                                       cGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAGGATCTGACAGa  <  2:514425/127‑1 (MQ=255)

                                                                                                                       cGTTTGCGCGGGCGCCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAGGATCTGACAGa  >  1:514425/1‑127 (MQ=255)

TCTTCAGGTTCAGAAACCTTCATTCATCATGACTATGTTCCAGTATTACAAACGATCACGGCATTTTGTTTTTTCAGCATTTATTGCTTTTGTTTTTGTCTTGTTATGCCAGAACACGGCGTTTGCGCGGGCGTCATCGAATGGTGATCTGCCGACAAAAGCGGACCTGCAGGCGCAACTTGACTCACTAAATAAACAAAAAGATCTTTCTGCTCAGGACAAACTGGTGCAGCAGGATCTGACAGA  >  NC_000913/486508‑486753

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A