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
A7 F123 I0 R1	46	52.8	1143652	95.1%	1087613	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	396,540	G→A	100%	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	99.4%	154.2 / ‑6.6	48	A208T (GCA→ACA)	USA300HOU_0364	possible lipoprotein
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (22/24); total (23/25)
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
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTA  >  CP000730/396410‑396670

tatCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAt                                                                                                                          >  1:477695/1‑141 (MQ=255)

   cATACCAAAATTAATGTTACAAGGATCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTa                                                                                                                       <  2:357941/141‑1 (MQ=255)

    aTACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTAt                                                                                                                      >  2:63090/1‑141 (MQ=255)

       ccAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGAc                                                                                                                   <  2:533490/141‑1 (MQ=255)

        cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                  >  1:441739/1‑141 (MQ=255)

        cAAAAATAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                  <  1:24933/141‑1 (MQ=255)

         aaaaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACtt                                                                                                                 <  1:204059/141‑1 (MQ=255)

            aTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTAtt                                                                                                              >  1:547918/1‑141 (MQ=255)

                aTGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaaa                                                                                                          >  2:291398/1‑141 (MQ=255)

                 tGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAc                                                                                                         >  2:397497/1‑141 (MQ=255)

                  gTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAcc                                                                                                        >  2:321211/1‑141 (MQ=255)

                  gTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAcc                                                                                                        >  2:125199/1‑141 (MQ=255)

                           ttCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTaga                                                                                               >  2:469201/1‑141 (MQ=255)

                                gtGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGACACACAAAAAATTTATGACTTATTTAAACCTATTTTAGATaaaa                                                                                          >  2:222799/2‑141 (MQ=255)

                                  gACCTATTAAATGAAGTTGCAACTTCTAAAATAACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGAACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaaaa                                                                                        >  1:548964/1‑141 (MQ=255)

                                   aCCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCAGACAAAAAAGTTATGACTTATTTAAACCTATTTTAGAGaacaagg                                                                                       >  2:309612/1‑139 (MQ=255)

                                    ccTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGa                                                                                      <  1:340891/141‑1 (MQ=255)

                                    ccTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGa                                                                                      <  1:340899/141‑1 (MQ=255)

                                    ccTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGa                                                                                      <  2:422046/141‑1 (MQ=255)

                                      tATTAAATGAAGTTGCAACTTCTAAAAGCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATa                                                                                    <  2:3950/141‑1 (MQ=255)

                                        ttAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATcaa                                                                                  >  1:180802/1‑141 (MQ=255)

                                          acaTGCAGTTGCAAGTTCTAACATCGGATGAGAAGAATAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaa                                                                                <  1:412117/139‑1 (MQ=255)

                                          aaaTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAACTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTAGAGGTACACAAAAAACTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaa                                                                                <  1:108793/141‑1 (MQ=255)

                                                     caattgcTAAACTTACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatg                                                                     <  1:351020/135‑1 (MQ=255)

                                                      aaCTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatga                                                                    <  1:263891/141‑1 (MQ=255)

                                                      aaCTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatga                                                                    >  1:522016/1‑141 (MQ=255)

                                                      aaCTTCTAAAAGCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatga                                                                    <  1:53874/141‑1 (MQ=255)

                                                         ttCGAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGatat                                                                 <  2:107253/141‑1 (MQ=255)

                                                           cTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGAtctca                                                               >  2:484631/1‑140 (MQ=255)

                                                           cTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATACGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATcc                                                               >  2:363681/1‑141 (MQ=255)

                                                              aaaTAACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAATCCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaaa                                                            <  2:176601/141‑1 (MQ=255)

                                                                  cacaGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGaa                                                        >  1:82145/1‑141 (MQ=255)

                                                                      ggTGAAGAAGACATTTATTCACATACAGATTATTAATTATGTAAAGCGCAGGCTGAATAATCTCGAAAAGGTGATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTc                                                    >  2:547146/1‑141 (MQ=255)

                                                                              agaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGACAAAAGATAAAAAATTAAGGGAGGAGATCCAAATGAACTTCGATAAAGt                                            >  1:271393/1‑141 (MQ=255)

                                                                                 aaTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGGTGATATCCAAATGAACTTCGATAAAGTGaa                                         >  2:361161/1‑141 (MQ=255)

                                                                                 aaTTTATTCAAATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTAGGACTTGTTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGaa                                         <  2:530165/141‑1 (MQ=255)

                                                                                             tACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAACAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAACAAATTACGTGATGATATCCAAATGAACTTCGATAAAGTGATTCAATTACTGGa                             <  1:402757/141‑1 (MQ=255)

                                                                                             tACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGa                             <  1:397497/141‑1 (MQ=255)

                                                                                             tACAGAATCATATGATTCTAAAGCGAACGATGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGa                             <  2:479350/141‑1 (MQ=255)

                                                                                              aCAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGAt                            <  1:163869/141‑1 (MQ=255)

                                                                                                          gATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGAt                <  2:95589/141‑1 (MQ=255)

                                                                                                               tAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaa           <  2:407285/141‑1 (MQ=255)

                                                                                                                  aGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg        <  1:321211/141‑1 (MQ=255)

                                                                                                                  aGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg        >  1:393534/1‑141 (MQ=255)

                                                                                                                  aGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg        <  2:548964/141‑1 (MQ=255)

                                                                                                                  aGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg        <  1:125199/141‑1 (MQ=255)

                                                                                                                      aaCGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGt    >  2:315632/1‑141 (MQ=255)

                                                                                                                        cGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTa  >  2:533282/1‑141 (MQ=255)

TATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTA  >  CP000730/396410‑396670

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A