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
A6 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	835,858	T→C	25.8%	C192C (TGT→TGC)	narH →	nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	835,858	0	T	C	25.8%	97.6 / 38.0	62	C192C (TGT→TGC)	narH	nitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand): ref base T (23/23); new base C (8/8); total (31/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.36e-01

TAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAT  >  minE/835789‑835927

taGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtg                                                                      <  1:3181309/71‑1 (MQ=255)

taGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtg                                                                      >  1:3336679/1‑71 (MQ=255)

taGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtg                                                                      <  1:1472040/71‑1 (MQ=255)

taGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgt                                                                       <  1:3621570/70‑1 (MQ=255)

 aGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtg                                                                      <  1:3689200/70‑1 (MQ=255)

  gCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtgt                                                                     <  1:3867308/70‑1 (MQ=255)

  gCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtgt                                                                     <  1:3018493/70‑1 (MQ=255)

   ccAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTgg                                                                   <  1:3039361/71‑1 (MQ=255)

    cAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGc                                                                  <  1:3913462/71‑1 (MQ=255)

     aGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTTCGAACACTGCCTGAA‑CCCGGCATGTGTGGc                                                                  >  1:349795/1‑70 (MQ=255)

     aGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGc                                                                  >  1:2971718/1‑70 (MQ=255)

     aGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGc                                                                  >  1:289658/1‑70 (MQ=255)

       ttCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGAc                                                               <  1:3779713/71‑1 (MQ=255)

       ttCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGAc                                                               <  1:1829041/71‑1 (MQ=255)

         tgAAAACACCTTCATTATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCt                                                             >  1:741533/2‑71 (MQ=255)

         tgAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCt                                                             >  1:2829823/2‑71 (MQ=255)

         cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGAcc                                                              <  1:3935453/70‑1 (MQ=255)

         cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGAcc                                                              <  1:2028352/70‑1 (MQ=255)

         cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCt                                                             >  1:2973485/1‑71 (MQ=255)

          gAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCg                                                                 <  1:333273/66‑1 (MQ=255)

          gAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCt                                                             <  1:834442/70‑1 (MQ=255)

           aaaaCACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGc                                                           <  1:2907425/71‑1 (MQ=255)

           aaaaCACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGc                                                           >  1:1628771/1‑71 (MQ=255)

            aaaCACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGAc                                                               >  1:3534493/1‑66 (MQ=255)

              acacCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGccc                                                         >  1:1145245/1‑70 (MQ=255)

                acCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAg                                                      >  1:1576109/1‑71 (MQ=255)

                  cTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCg                                                    <  1:3489727/71‑1 (MQ=255)

                  cTTCATGATGTACCTGCCTCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCg                                                    <  1:3854788/71‑1 (MQ=255)

                   ttCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCg                                                                 <  1:961350/57‑1 (MQ=255)

                    tCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGt                                                  >  1:740119/1‑71 (MQ=255)

                    tCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGt                                                  >  1:2237282/1‑71 (MQ=255)

                     cATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCggcg                                                 >  1:1591014/1‑69 (MQ=255)

                      atgatgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCggcg                                                 <  1:231505/70‑3 (MQ=255)

                       tgatgTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCg                                                                 <  1:2988497/53‑1 (MQ=255)

                       tgatgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGGGGCGACCTGCCCAAGCGgcgc                                                <  1:2500398/70‑1 (MQ=255)

                         atgTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGAc                                                               >  1:3899069/1‑53 (MQ=255)

                         atgTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGAt                                             <  1:2439608/71‑1 (MQ=255)

                         atgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCgg                                                   >  1:2599389/1‑65 (MQ=255)

                         atgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTAt                                             >  1:2411484/1‑71 (MQ=255)

                          tgTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGAtt                                            <  1:2838530/71‑1 (MQ=255)

                            tATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtg                                                                      <  1:181752/43‑1 (MQ=255)

                            tATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCg                                                    <  1:3267660/61‑1 (MQ=255)

                                  ccGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACg                                    <  1:1166262/71‑1 (MQ=255)

                                  ccGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACg                                    >  1:3538935/1‑71 (MQ=255)

                                  ccGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACg                                    >  1:1358102/1‑71 (MQ=255)

                                      gcCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTg                                  >  1:2514634/1‑69 (MQ=255)

                                         tgtgCGAACACTGCCTGAA‑CCCGGCATGTGTGGCg                                                                 <  1:1621716/35‑1 (MQ=255)

                                          gtgCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaag                               >  1:1263113/1‑68 (MQ=255)

                                           tgCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                             <  1:2287669/69‑1 (MQ=255)

                                           tgCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaag                               >  1:2721897/1‑67 (MQ=255)

                                           tgCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGaagaag                            <  1:3641584/70‑1 (MQ=255)

                                           tgCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACGCgaagaa                             <  1:137544/69‑1 (MQ=255)

                                           tgCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACGCgaagaa                             <  1:1615586/69‑1 (MQ=255)

                                              gAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGccc                                                         >  1:1578968/1‑38 (MQ=255)

                                              gAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACgcg                                  <  1:999948/61‑3 (MQ=255)

                                               aaCACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATgg                        >  1:2532054/1‑70 (MQ=255)

                                               aaCACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATgg                        >  1:3889425/1‑70 (MQ=255)

                                               aaCACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATgg                        >  1:1490961/1‑70 (MQ=255)

                                                acacTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACGCGAAGAAGACGGCa                      <  1:1259087/71‑1 (MQ=255)

                                                 cacTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCAt                     >  1:3423891/1‑71 (MQ=255)

                                                 cacTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCAt                     >  1:3385341/1‑71 (MQ=255)

                                                    tGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGt                  >  1:499022/1‑71 (MQ=255)

                                                      ccTGAA‑CCCGGCATGTGTGGCGAGCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTc                 <  1:3077938/70‑1 (MQ=255)

                                                      ccTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTAc                                         <  1:539961/46‑1 (MQ=255)

                                                       cTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCt               <  1:3603997/71‑1 (MQ=255)

                                                          aa‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGa             <  1:1373010/70‑1 (MQ=255)

                                                             cccGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCg          <  1:982906/71‑1 (MQ=255)

                                                               cGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAc        >  1:3930504/1‑71 (MQ=255)

                                                                 gCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTc                 >  1:3153570/1‑60 (MQ=255)

                                                                  cATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAg     >  1:1687624/1‑71 (MQ=255)

                                                                    tgtgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTgaagaa                             <  1:913346/45‑1 (MQ=255)

                                                                      tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAgaga  >  1:1414510/1‑67 (MQ=255)

                                                                      tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt  <  1:3621278/70‑1 (MQ=255)

TAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAT  >  minE/835789‑835927

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A