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
A13 F20 I0 R1	91	60.0	1338914	94.3%	1262595	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,143,110	G→A	33.1%	V163V (GTG→GTA)	USA300HOU_2026 →	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,143,110	0	G	A	33.1%	42.2 / 30.8	45	V163V (GTG→GTA)	USA300HOU_2026	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base G (15/15); new base A (9/6); total (24/21)
Fisher's exact test for biased strand distribution p-value = 7.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.37e-01

AGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCTGTTCCAAT  >  CP000730/2142974‑2143250

aGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCAt                                                                                                                                          <  2:81949/141‑1 (MQ=255)

aGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCAt                                                                                                                                          <  2:429241/141‑1 (MQ=255)

 gCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCAtt                                                                                                                                         >  2:432147/1‑141 (MQ=255)

   tAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCGtttt                                                                                                                                       >  1:583062/1‑140 (MQ=255)

   tAATTATTATTGCTCGAAAAATACCTATATTTAGCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATTCGATTAAAGGTAATCGTATCGTGGCGtttt                                                                                                                                       >  1:348/1‑140 (MQ=255)

    tattattgttGCTCGAAAAATACCTATATTTATTTTCTTTGTATCTATTAGTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATttat                                                                                                                                      <  2:55607/140‑1 (MQ=255)

        attattGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCATTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGCGAATTATTTAATGCGATTAAAGGTAATCGTATAGTAGCATttattctg                                                                                                                                  >  1:183597/1‑138 (MQ=255)

         taaaaaaaaaaaaaaTACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTg                                                                                                                                 <  2:161706/131‑1 (MQ=255)

          tattGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGc                                                                                                                                >  2:566917/1‑141 (MQ=255)

            ttGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTa                                                                                                                              >  1:300185/1‑141 (MQ=255)

                    aaaaTACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTa                                                                                                                      >  2:88565/1‑141 (MQ=255)

                               atTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAat                                                                                                           <  1:432147/141‑1 (MQ=255)

                                    tcttctTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTg                                                                                                      <  2:243813/141‑1 (MQ=255)

                                     tttgtttGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTAAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAAAAGTAAGTTCCGTTATATTTGc                                                                                                     <  2:329614/137‑1 (MQ=255)

                                        cttTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCAtt                                                                                                  >  1:461300/1‑141 (MQ=255)

                                           tGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGc                                                                                               >  1:547361/1‑141 (MQ=255)

                                             tATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGcac                                                                                             >  2:386642/1‑141 (MQ=255)

                                               tCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACAt                                                                                           >  1:207202/1‑141 (MQ=255)

                                                 tattatTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTGATTAATATTTGCCTTAAAACATaa                                                                                         >  2:335363/1‑141 (MQ=255)

                                                           ccTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGTAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCaaa                                                                               <  2:614721/141‑1 (MQ=255)

                                                            cTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAAt                                                                              >  1:6784/1‑141 (MQ=255)

                                                              ttattaGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAAttt                                                                            >  2:663077/1‑141 (MQ=255)

                                                                attaGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAAACGTATCGTGGCATTTATTATGGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACAGAACACTTTCAAGtttgt                                                                          >  2:571684/1‑139 (MQ=255)

                                                                 ttaGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCAGATAATGATTTCAAATTTAtt                                                                         >  1:202787/1‑141 (MQ=255)

                                                                     aagaaTATGTATTCAGAAATGTATTCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAg                                                                     <  2:97395/141‑1 (MQ=255)

                                                                      agaaTATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGt                                                                    <  2:240949/141‑1 (MQ=255)

                                                                                ttCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTCCAGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCAATAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGt                                                          >  1:387281/1‑141 (MQ=255)

                                                                                ttCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGt                                                          >  1:574125/1‑141 (MQ=255)

                                                                                       aaGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGgtg                                                   <  1:335363/141‑1 (MQ=255)

                                                                                          tAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCa                                                <  2:142051/141‑1 (MQ=255)

                                                                                           aaTCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCCGTTTATTTTGGTATGGGTGTCAt                                               >  2:192571/1‑141 (MQ=255)

                                                                                           aaTCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCAt                                               >  2:648478/1‑141 (MQ=255)

                                                                                                     gaATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTCTGGGAGTCATTTTTTCATTa                                     >  1:639434/1‑141 (MQ=255)

                                                                                                      aaTTATTTAAGGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAg                                    <  2:74083/141‑1 (MQ=255)

                                                                                                       atttttTAAAGTGATTAAAGGTAAGCGTATCGTGGCATTTATTATTTCCACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGc                                   <  2:47879/141‑1 (MQ=255)

                                                                                                       attattTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGc                                   <  2:335810/141‑1 (MQ=255)

                                                                                                          attTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTACTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCata                                >  2:608400/1‑141 (MQ=255)

                                                                                                          attTAATGCGATTAAAGGTAATCGTATCGTAGCAGTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCata                                <  1:229856/141‑1 (MQ=255)

                                                                                                                tGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTg                          <  1:110591/141‑1 (MQ=255)

                                                                                                                tGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTg                          <  1:293693/141‑1 (MQ=255)

                                                                                                                   gATTAAAGGTAATCGTATCGTGGCATTTATGATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATATCAAATTTATTCCACTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGAc                       <  2:273869/141‑1 (MQ=255)

                                                                                                                    aTTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACa                      <  2:288964/141‑1 (MQ=255)

                                                                                                                          ggTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAACATATGTTTGGACAAAACgg                >  2:114226/1‑141 (MQ=255)

                                                                                                                            tAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCt              <  2:316989/141‑1 (MQ=255)

                                                                                                                                 gtatcgtAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCTg         >  2:426287/1‑141 (MQ=255)

                                                                                                                                        ggCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTTTTTTTTTTTTTTTTTGACAAAACGGCTTGCTGTTCCAat  >  2:120888/1‑141 (MQ=255)

AGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCTGTTCCAAT  >  CP000730/2142974‑2143250

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A