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
A9 F174 I1 R2	22	37.9	845450	92.3%	780350	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	396,540	G→A	A208T (GCA→ACA)	USA300HOU_0364 →	possible lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	396,540	0	G	A	86.1%	115.7 / 2.4	43	A208T (GCA→ACA)	USA300HOU_0364	possible lipoprotein
Reads supporting (aligned to +/- strand): ref base G (2/4); new base A (19/18); total (21/22)
Fisher's exact test for biased strand distribution p-value = 6.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTC  >  CP000730/396404‑396676

aTTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGcacaca                                                                                                                                      >  2:244246/1‑141 (MQ=255)

  tAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACaaa                                                                                                                                    >  2:367629/1‑141 (MQ=255)

           tACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATg                                                                                                                           >  1:169232/1‑141 (MQ=255)

            aCCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGa                                                                                                                          <  1:107794/141‑1 (MQ=255)

             ccAAAATTAATGTTACAAAATACTGTAGAAATATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAAAAAAAAAAAAAATTTATGAc                                                                                                                         <  2:171976/141‑1 (MQ=255)

              cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                        <  1:39824/141‑1 (MQ=255)

              cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                        <  1:24841/141‑1 (MQ=255)

              cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                        <  2:68351/141‑1 (MQ=255)

                aaaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTa                                                                                                                      >  1:208414/1‑141 (MQ=255)

                aaaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTa                                                                                                                      >  1:208442/1‑141 (MQ=255)

                    tAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTa                                                                                                                  >  1:90288/1‑141 (MQ=255)

                      aTGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaaa                                                                                                                >  1:328458/1‑141 (MQ=255)

                        gTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGAAGAAAAAAAAATTTATGACTTATTTAAAcc                                                                                                              <  2:120945/141‑1 (MQ=255)

                            cAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTAtt                                                                                                          >  1:167390/1‑141 (MQ=255)

                               ggTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTa                                                                                                       <  1:85377/141‑1 (MQ=255)

                                        gACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaaaa                                                                                              >  1:70649/1‑141 (MQ=255)

                                                  aTGAAGTTGCAACTGCTAAAATAACAGGGGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGTGAACGTTGAAAAAGAACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAAt                                                                                    <  2:333754/141‑1 (MQ=255)

                                                    gAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTa                                                                                  >  1:91869/1‑141 (MQ=255)

                                                     aaatagaaaCTCCAAAAATAAAAGATGAACAACAAATCTATTAACATACAAATTAAAATGAATATAAAGCGAACGATGAAGGCACACAAAAAAATAATGACTAAATTAAAAAAATTTAAAAAAAAAAAGATAAAAAATTaa                                                                                 <  2:208414/134‑1 (MQ=255)

                                                     aaGTTGCAAAATATAAAATCACAGGTGAAGAAGAAATTTATTCACATAAAGATTTATATGAGTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTCAACTTTGTTTAGAGAAAAAAAAAAAAAAATTaa                                                                                 <  2:208442/141‑1 (MQ=255)

                                                              atgaaaaattaaaaGGAGAATAAGAAAATGCATCATATACAACTGTATAGTATTTGAAAGCGGCAATTGACGCCGCATAAAAAATTTCAGTCTTTTTTATACCAATTTTACATAAAAAAGATAAAAAATTAAGTGATGata                                                                        <  2:354424/128‑1 (MQ=255)

                                                                   aaaaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaa                                                                   >  2:33680/1‑141 (MQ=255)

                                                                     aaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAAt                                                                 >  1:265298/1‑141 (MQ=255)

                                                                     aaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAAAAAAAAGATAAAAAATTAAGTGATGATATCCAAAt                                                                 <  2:169232/141‑1 (MQ=255)

                                                                       acacaGGTGAAGAAGAAATTTATTCACATACAGATTTATATTATTTTAAAGCGAACGTTGAAAAAAAAAAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGa                                                               <  2:63800/140‑1 (MQ=255)

                                                                         acaGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAAc                                                             >  1:113415/1‑141 (MQ=255)

                                                                           aGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACtt                                                           <  2:412809/141‑1 (MQ=255)

                                                                                  gaagaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATaaa                                                    <  2:86433/141‑1 (MQ=255)

                                                                                    agaaATTTATTCACATACAGCTTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAAATAAGTGATGATATCCAAATGAACTTCGATAAAgg                                                  >  1:61295/1‑140 (MQ=255)

                                                                                        aTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAAt                                              >  1:91797/1‑141 (MQ=255)

                                                                                         tttATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATc                                             <  1:314868/141‑1 (MQ=255)

                                                                                            aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAat                                          >  1:21388/1‑141 (MQ=255)

                                                                                            aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAat                                          >  1:52473/1‑141 (MQ=255)

                                                                                               cacaTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAattat                                       <  2:243437/141‑1 (MQ=255)

                                                                                                 cagaCAGAGTTATAGGATTTTAAAGCGAACGGTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTg                                     >  2:153163/4‑141 (MQ=255)

                                                                                                   tACAGATTTATATTATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGa                                   <  1:159834/141‑1 (MQ=255)

                                                                                                   tACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGa                                   <  1:159861/141‑1 (MQ=255)

                                                                                                    aCAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGAt                                  <  2:93921/141‑1 (MQ=255)

                                                                                                    aCAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGAt                                  <  1:387831/141‑1 (MQ=255)

                                                                                                     cAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATa                                 >  2:184034/1‑141 (MQ=255)

                                                                                                     cAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATa                                 >  1:155090/1‑141 (MQ=255)

                                                                                                        aTTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAat                              >  1:210679/1‑141 (MQ=255)

                                                                                                                                    aGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTc  >  2:208193/1‑141 (MQ=255)

                                                                                                                                    aGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTc  <  1:153163/141‑1 (MQ=255)

ATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTC  >  CP000730/396404‑396676

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

GATK/CNVnator alignment

N/A