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 F22 I0 R2	95	29.9	669916	92.3%	618332	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	396,540	G→A	86.7%	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	86.7%	102.9 / 6.8	44	A208T (GCA→ACA)	USA300HOU_0364	possible lipoprotein
Reads supporting (aligned to +/- strand): ref base G (2/4); new base A (19/19); total (21/23)
Fisher's exact test for biased strand distribution p-value = 6.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCA  >  CP000730/396400‑396677

aTACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGgcg                                                                                                                                           >  2:153873/1‑141 (MQ=255)

    aTTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAACTGAAGTTGCAACTTCTAAAATCTCAGGTGATGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGcacaca                                                                                                                                       <  1:113920/141‑1 (MQ=255)

        gATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACaaaaa                                                                                                                                   >  2:45222/1‑141 (MQ=255)

                 ccAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGAc                                                                                                                          <  1:181476/141‑1 (MQ=255)

                         aaTGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTTAAGGCACACAAAAAATTTATGACTTATTTaa                                                                                                                  >  2:300043/1‑141 (MQ=255)

                         aaTGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaa                                                                                                                  <  1:193319/141‑1 (MQ=255)

                            gTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAGCGTTGAAGGCAAACAAAAAATTTATGACTTATTTAAAcc                                                                                                               <  2:54425/141‑1 (MQ=255)

                            gTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAAcc                                                                                                               <  1:93208/141‑1 (MQ=255)

                            gTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAcc                                                                                                               <  2:77964/141‑1 (MQ=255)

                                    gTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTag                                                                                                       <  1:289968/141‑1 (MQ=255)

                                       cTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAgaga                                                                                                    >  1:112941/1‑141 (MQ=255)

                                        tGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaa                                                                                                   >  1:270518/1‑141 (MQ=255)

                                            gACCTATTAAATGAAGTTGCAACTTCTAAAAGCACATGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaaaa                                                                                               <  1:2255/141‑1 (MQ=255)

                                                 aTTAAATGAAGTTGCAACTTCTAAAATCACAGGTGCAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAAGCACACAAAAAATTTATGCCTTATTTAAACCTATTTTAGAGAAAAATGATaa                                                                                          >  2:290200/1‑141 (MQ=255)

                                                  ttAAATGAAGTTGAAACTTCTAAAATAAAAGATGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGGTGAAGACACACAAAAAATTTATGACTTATTTAAACCAAATAAAAAAAAAAAAGATaaa                                                                                         <  2:314031/141‑1 (MQ=255)

                                                        gAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTa                                                                                   <  1:95936/141‑1 (MQ=255)

                                                        gAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTa                                                                                   >  2:110494/1‑141 (MQ=255)

                                                          aGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAg                                                                                 >  1:170093/1‑141 (MQ=255)

                                                          aGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAg                                                                                 >  1:275328/1‑141 (MQ=255)

                                                           gTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGt                                                                                >  1:117812/1‑141 (MQ=255)

                                                             tGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtga                                                                              >  2:235854/1‑141 (MQ=255)

                                                              gCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                             >  2:135490/1‑141 (MQ=255)

                                                              gCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGACACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                             <  2:334289/141‑1 (MQ=255)

                                                                aaCTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatga                                                                           <  1:276026/141‑1 (MQ=255)

                                                                aaCTTCTAAAATCAAAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAAAAAAAAAATTAAGtgatga                                                                           <  2:15716/141‑1 (MQ=255)

                                                                        aaaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGACACAAAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaaa                                                                   <  2:12171/141‑1 (MQ=255)

                                                                             acaGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAAc                                                              >  2:127915/1‑141 (MQ=255)

                                                                              aaGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAAAAAAAAAAAAAATTTATGACTTATTTAAACCTATATTAAAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACt                                                             <  2:307310/140‑1 (MQ=255)

                                                                                 gTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCg                                                          >  2:172206/1‑141 (MQ=255)

                                                                                   gaagaagaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGAt                                                        <  1:102252/141‑1 (MQ=255)

                                                                                   gaagaagaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGAt                                                        <  2:16081/141‑1 (MQ=255)

                                                                                             tttATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATc                                              <  1:9745/141‑1 (MQ=255)

                                                                                              ttATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCa                                             >  1:110490/1‑141 (MQ=255)

                                                                                                aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAAt                                                                                     <  2:170160/99‑1 (MQ=255)

                                                                                                aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAAt                                                                                     >  1:170160/1‑99 (MQ=255)

                                                                                                aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAat                                           >  2:33595/1‑141 (MQ=255)

                                                                                                        aCAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGAt                                   >  1:178411/1‑141 (MQ=255)

                                                                                                           aagttATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATaaa                                <  2:173987/138‑1 (MQ=255)

                                                                                                            aTTTATATGATTTTAAAGCGAACGTTGAAAACACAAAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAat                               <  2:114307/141‑1 (MQ=255)

                                                                                                                   tGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGa                        >  2:299415/1‑141 (MQ=255)

                                                                                                                        ttAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaaca                   <  1:45222/141‑1 (MQ=255)

                                                                                                                            aGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg               >  1:175179/1‑141 (MQ=255)

                                                                                                                             gCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcggc              >  2:290902/1‑141 (MQ=255)

                                                                                                                                   gTTGAAGGCGCACAAAAAATTTATGACTTATTTATTGCTATTTGAGAGAATAAAGTTAATAAATTAAGTGATGATATACAAATGAATTTCAATAAAGTTTGTCAATTATTGGATAAATAGACTGTTTACAACGGCGGTTAt        <  2:105392/141‑1 (MQ=255)

                                                                                                                                      gAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAg     >  2:181304/1‑141 (MQ=255)

                                                                                                                                         ggCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCa  <  2:169761/141‑1 (MQ=255)

ATACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCA  >  CP000730/396400‑396677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A