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	835,846	G→C	20.9%	L188L (CTG→CTC)	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	835,846	0	G	C	20.9%	163.1 / 37.0	81	L188L (CTG→CTC)	narH	nitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand): ref base G (30/34); new base C (9/8); total (39/42)
Fisher's exact test for biased strand distribution p-value = 7.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

AGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCT  >  minE/835776‑835914

aGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTg                                                                       <  1:945051/71‑1 (MQ=255)

aGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTg                                                                       <  1:940361/71‑1 (MQ=255)

aGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTg                                                                       <  1:489827/71‑1 (MQ=255)

 gAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGa                                                                      <  1:374529/71‑1 (MQ=255)

   aGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑c                                                                   >  1:1848602/1‑71 (MQ=255)

   aGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑c                                                                   <  1:135266/71‑1 (MQ=255)

     gCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑ccc                                                                 <  1:3876236/71‑1 (MQ=255)

      cGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCg                                                                >  1:3273268/1‑71 (MQ=255)

         tGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCa                                                             >  1:2271441/1‑71 (MQ=255)

         tGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCa                                                             >  1:2081803/1‑71 (MQ=255)

           tataGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtg                                                           >  1:2041892/1‑71 (MQ=255)

           tataGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAt                                                            <  1:1593906/70‑1 (MQ=255)

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

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

             taGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtg                                                         >  1:3336679/1‑71 (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)

                  aGTTTGAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAA‑tccca                                                               >  1:1090451/1‑58 (MQ=255)

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

                  aGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑cc                                                                  >  1:3218393/1‑57 (MQ=255)

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

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

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

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

                     tCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCgg                                                               >  1:2069830/1‑57 (MQ=255)

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

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

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

                      cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGAcc                                                 <  1:3935453/70‑1 (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‑CCCgg                                                               <  1:1960819/54‑1 (MQ=255)

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

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

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

                          aaCACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGc                                                              >  1:2851102/1‑53 (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                                     >  1:2237282/1‑71 (MQ=255)

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

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

                                   atgatgTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCgg                                                               >  1:875595/1‑43 (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‑CCCGGc                                                              <  1:2487162/41‑1 (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                       >  1:3538935/1‑71 (MQ=255)

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

                                               ccGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGGCGCTATCTACAAACg                       <  1:1166262/71‑1 (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                <  1:1615586/69‑1 (MQ=255)

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

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

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

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

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

                                                            aaCACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATgg           >  1:2532054/1‑70 (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)

AGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCT  >  minE/835776‑835914

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A