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 F999 I0 R1	92	76.2	6048880	97.1%	5873462	49.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,948,805	(G)_6→7	coding (1165/1521 nt)	yifB ←	putative magnesium chelatase YifB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,948,799	1	.	G	96.3%	205.6 / 1.1	54	coding (1171/1521 nt)	yifB	putative magnesium chelatase YifB
Reads supporting (aligned to +/- strand): ref base . (0/2); new base G (25/27); total (25/29)
Fisher's exact test for biased strand distribution p-value = 4.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAACGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑GGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTCG  >  NC_000913/3948751‑3948842

tAACGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑cc                                               <  1:5694742/49‑1 (MQ=255)

tAACGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑cc                                               <  1:4090091/49‑1 (MQ=255)

tAACGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑cc                                               <  1:235139/49‑1 (MQ=255)

tAACGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑g                                             >  1:2907/1‑50 (MQ=255)

 aaCGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑g                                             <  1:3022770/49‑1 (MQ=255)

  aCGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑gg                                            <  1:668832/49‑1 (MQ=255)

   cGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑gggg                                          >  1:667596/1‑50 (MQ=255)

   cGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑gggg                                          >  1:2840080/1‑50 (MQ=255)

    ggTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑ggggg                                         >  1:2534825/1‑50 (MQ=255)

    ggTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑ggggg                                         <  1:5129604/50‑1 (MQ=255)

     gTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑ggggg‑g                                       <  1:4598384/50‑1 (MQ=255)

      tGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑ggggg‑gg                                      >  1:5347653/1‑49 (MQ=255)

        gcgcTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑ggggg‑ggt                                     <  1:4195483/49‑3 (MQ=255)

        gcgcTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑ggggg‑ggt                                     <  1:4947818/49‑3 (MQ=255)

           ctgctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTa                                  <  1:450033/50‑1 (MQ=255)

            tgctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTaa                                 >  1:2126198/1‑50 (MQ=255)

             gctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAAt                                >  1:5296142/1‑50 (MQ=255)

             gctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAAt                                >  1:5027379/1‑50 (MQ=255)

              ctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTaa                                 <  1:5808015/48‑1 (MQ=255)

              ctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTaa                                 <  1:2889518/48‑1 (MQ=255)

              ctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTaa                                 <  1:2786045/48‑1 (MQ=255)

              ctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTaa                                 <  1:5948775/48‑1 (MQ=255)

              ctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAAt                                <  1:4423391/49‑1 (MQ=255)

              ctTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATg                               <  1:897549/50‑1 (MQ=255)

                ttCTCCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GAGGTAATgg                              >  1:3524092/1‑49 (MQ=255)

                 tctcCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATgg                              <  1:1241299/48‑1 (MQ=255)

                 tctcCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGa                            >  1:2364943/1‑50 (MQ=255)

                  ctcCCGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGa                            <  1:3300967/49‑1 (MQ=255)

                    cccGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGAtct                         >  1:3038187/1‑50 (MQ=255)

                     ccGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGAtctc                        >  1:4700671/1‑50 (MQ=255)

                     ccGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGAt                           <  1:2202448/47‑1 (MQ=255)

                      cGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGAtctc                        >  1:3389287/1‑49 (MQ=255)

                      cGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGAtctc                        >  1:3604375/1‑49 (MQ=255)

                      cGGCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTcc                       <  1:1276160/50‑1 (MQ=255)

                       ggCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGAtctc                        >  1:4441500/1‑48 (MQ=255)

                        gCACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAg                     <  1:1034597/50‑1 (MQ=255)

                         cACTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGt                    >  1:3038528/1‑50 (MQ=255)

                          aCTACCGTTTTACTCAAAATGTCG‑GGGGG‑GTGGTAATGGGATCTCCAGTg                   <  1:4859833/50‑1 (MQ=255)

                          aCTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGt                    >  1:6029405/1‑49 (MQ=255)

                          aCTACCGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGt                    >  1:4951904/1‑49 (MQ=255)

                              ccGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTgaga                <  1:4768883/49‑1 (MQ=255)

                              ccGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTgaga                <  1:5866843/49‑1 (MQ=255)

                               cGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTgagaga              <  1:2773553/50‑1 (MQ=255)

                               cGTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTga                  >  1:527004/1‑46 (MQ=255)

                                gTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTga                  >  1:4809880/1‑45 (MQ=255)

                                gTTTTACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGAt             <  1:1691097/50‑1 (MQ=255)

                                 ttttACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATc            <  1:5161572/50‑1 (MQ=255)

                                 ttttACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATc            <  1:1144747/50‑1 (MQ=255)

                                 ttttACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATc            <  1:1332170/50‑1 (MQ=255)

                                 ttttACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATc            <  1:2613065/50‑1 (MQ=255)

                                  tttACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATc            >  1:3235385/1‑49 (MQ=255)

                                   ttACTCAAAATG‑CC‑GGGGGTGTGGTAATGGGATCTCCAGTGAGAGATCg           <  1:3856094/49‑1 (MQ=255)

                                    tACTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCg           >  1:3489088/1‑48 (MQ=255)

                                     aCTCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGaa         <  1:976375/49‑1 (MQ=255)

                                       tCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCg      >  1:5685364/1‑50 (MQ=255)

                                       tCAAAATG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCg      >  1:4780861/1‑50 (MQ=255)

                                         aaaaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCgg     <  1:74195/49‑1 (MQ=255)

                                         aaaaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCg      <  1:3502361/48‑1 (MQ=255)

                                         aaaaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCg      <  1:4830068/48‑1 (MQ=255)

                                         aaaaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGt    <  1:2307312/50‑1 (MQ=255)

                                          aaaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTc   <  1:5593337/50‑1 (MQ=255)

                                          aaaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTc   >  1:3164803/1‑50 (MQ=255)

                                          aaaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTc   >  1:2675096/1‑50 (MQ=255)

                                           aaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTc   >  1:5505234/1‑49 (MQ=255)

                                           aaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTc   >  1:1389626/1‑49 (MQ=255)

                                           aaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTc   >  1:512847/1‑49 (MQ=255)

                                           aaTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTCg  <  1:2828596/50‑1 (MQ=255)

                                            aTG‑CCGGGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTc   >  1:555368/1‑48 (MQ=255)

TAACGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATG‑CC‑GGGGG‑GTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTCG  >  NC_000913/3948751‑3948842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A