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
A3 F76 I1 R1	29	54.3	2299912	90.6%	2083720	142.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,785,179	A→T	I645N (ATC→AAC)	ppsA ←	phosphoenolpyruvate synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,785,179	0	A	T	96.1%	134.6 / NA	53	I645N (ATC→AAC)	ppsA	phosphoenolpyruvate synthetase
Reads supporting (aligned to +/- strand): ref base A (1/0); major base T (16/33); minor base G (2/0); total (20/33)
Fisher's exact test for biased strand distribution p-value = 1.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGAACTGCTCGGCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTTCTC  >  NC_000913/1785039‑1785312

ggcaCTGCTCGGCCAGCACGGCGTCGGACGCGATTTCACACATCCTTATTAGTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTc                                                                                                                                     <  2:31067/140‑1 (MQ=255)

     tGCTCGGCCAGCAAGGCGTTGGCCGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGAt                                                                                                                                <  1:636366/143‑1 (MQ=255)

      gCTCGGCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCCCCAGTTCTGCAGTCGCCGCTTTCGCCTGCTCCACGGGACGCACGCACCGGCTCACGagc                                                                                                                               >  2:992061/1‑141 (MQ=255)

         cGGCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCa                                                                                                                            >  1:117771/1‑143 (MQ=255)

         cGGCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCa                                                                                                                            <  2:471679/143‑1 (MQ=255)

          ggCCAGGAAGGCGTTGGACGGGATTTCACACATCAGGATGATTTTCAGCCCGTTCTCGCTACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCaa                                                                                                                           <  2:564639/143‑1 (MQ=255)

          ggCCAGCAAGGCGTTGGACGGGATTTCAAACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGCACGCACGAACGGGTTAATGATCTCaa                                                                                                                           >  2:597875/1‑143 (MQ=255)

            ccAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCCCGAACGGGTCCATGACCTCCAcc                                                                                                                         >  2:655585/1‑142 (MQ=255)

               tcgagccGTGGGACGGGATTTCACACAGCATGATGATTTTCCGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTg                                                                                                                      <  1:661340/137‑1 (MQ=255)

               gCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACTGTACGCACGAACGGGTTCATGATCTCAACGTTg                                                                                                                      <  2:514769/143‑1 (MQ=255)

                cAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGGTCATGATCTCAACGTTgg                                                                                                                     >  1:664726/1‑143 (MQ=255)

                      gTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGCTCTACGTGTCGCACGAATGGGTCTCTTATCTCCTCGTTGGGCAGta                                                                                                               >  1:98051/1‑142 (MQ=255)

                          gACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGTCCCag                                                                                                           >  2:26900/1‑142 (MQ=255)

                           aCGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTGTCGCCTGATCTACGCTACGCACGAACGGGGTCATGATCTCACCGTTGGTCAGTCCCATg                                                                                                          >  1:253305/1‑143 (MQ=255)

                                     acacaTCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGca                                                                                                >  1:1051311/1‑143 (MQ=255)

                                      cacaTCATAATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGcac                                                                                               <  1:118472/143‑1 (MQ=255)

                                       acaTCATGATGATTTGCAGCCCGTTCTCGCCACGTTTCAGGCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGcaca                                                                                              <  1:1042753/143‑1 (MQ=255)

                                            atgatgATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGttt                                                                                         <  2:117771/143‑1 (MQ=255)

                                               ctcactttCCGCCCGTTCTCGCCACGTGTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCAc                                                                                      <  2:962652/138‑1 (MQ=255)

                                                     ttCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTTAACCACCTCTTTCGCCTGATCTACGGTACTCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTc                                                                                <  2:785557/143‑1 (MQ=255)

                                                        aGCCCGTTCTCGCCACGTCTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTcaca                                                                             <  1:297489/143‑1 (MQ=255)

                                                          cccGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTCCGATACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGGTTCACTGCTTCACACt                                                                           >  2:573888/1‑143 (MQ=255)

                                                           ccGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTc                                                                          <  1:340004/143‑1 (MQ=255)

                                                                ctcGCCAGGTTTCAGCCACTGCCGCGCCAGTTAGTCAACCGACGCTTCCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGGCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAgag                                                                     <  1:1095805/143‑3 (MQ=255)

                                                                 tcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGt                                                                                                                    <  2:1113738/95‑1 (MQ=255)

                                                                 tcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGt                                                                                                                    >  1:1113738/1‑95 (MQ=255)

                                                                 tcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAgcgc                                                                    <  1:214877/143‑1 (MQ=255)

                                                                   gCCACGTTTCCGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGa                                                                  <  2:415224/143‑1 (MQ=255)

                                                                    ccACGTTTCAGCCCCTGACGCGCCAGTTCGTCAACCACCGCTTTCGCCTGATCTAGGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGGCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGaa                                                                 <  2:369899/143‑1 (MQ=255)

                                                                          ttCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTc                                                           <  2:774114/143‑1 (MQ=255)

                                                                          ttCAGACCCTTCCTCTCCCGTTCTTCAACGCCCGCTTTCGCCTGTTCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTc                                                           <  2:1043616/143‑1 (MQ=255)

                                                                            cAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGAGCTACGGTACGCCCGAACGGGTTCATGATCTCAACGTTGGTTAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTcgc                                                         <  2:570393/143‑1 (MQ=255)

                                                                            cAGCCCCTGACGCGCCAGTCCTTCAACCCCCGCTTTCGCCTGAACTACGGTACGCACGGACGGGTTCATGATCGCAACGTCGGTCAGTCCCACGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTcgc                                                         <  2:866578/143‑1 (MQ=255)

                                                                                 ccTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGCACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCGTCACACTCCAGCGCGACACCGCCGCGGagg                                                    >  2:780217/1‑141 (MQ=255)

                                                                                     tcgcgCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGt                                                <  2:195704/142‑1 (MQ=255)

                                                                                     aCGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACGCCAGCGCGAAACAGTCGCGGAAGCTGt                                                <  2:476627/143‑1 (MQ=255)

                                                                                         gcCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGa                                            >  2:359309/1‑143 (MQ=255)

                                                                                           cAGTTCTTCAATCACCGCTTTCGCTCGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTGGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGaaa                                          <  2:968000/143‑1 (MQ=255)

                                                                                             gTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACCCCAGCGCGACACAGTCGCGCACGCTGCCGGAAACa                                        >  2:1145100/1‑143 (MQ=255)

                                                                                             gTTCTTCAACCACCGCTTTCGCCTGATCGACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACa                                        <  1:937659/143‑1 (MQ=255)

                                                                                                cttcAACCACCGCTTTCGCCCGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAg                                     <  1:341587/143‑1 (MQ=255)

                                                                                                  tcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAACCATcgcg                                   >  1:12940/1‑143 (MQ=255)

                                                                                                        accGCTTTCGCCTGATCTAAGGAACGAACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGCCGTTGCGCACACCTTTCACTGCTTCACACCACAGCGCCAAACAGCCACGGCAGCTCTCGGAAAACCAGCGGCCcgc                             >  2:201867/1‑143 (MQ=255)

                                                                                                              ttCGCCTGGTCTGCGGTCCGTCGGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCTTGTCGTTGCGCACACGTTTCCCGGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACg                       <  2:630768/143‑1 (MQ=255)

                                                                                                                     gATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACATTGCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTAGGAGACATAGCGGCCCGCGCCACGGAAGCCg                >  2:681904/1‑143 (MQ=255)

                                                                                                                           cGGTACGCACGAACGGGTTCCTGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGGTTCACACTCCAGCGCGGAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGCAGCCgcgactc          >  2:536211/1‑137 (MQ=255)

                                                                                                                            tttacttaCGAACGGGTTCACGAGCTCAACGCTGGCCCGCCCCATGCCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCg         <  1:597875/136‑1 (MQ=255)

                                                                                                                            ggTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCCCTGCTTCACACTCCACCGCGAAACAGTCGCGGAAGCTGTCGGAAACACCGCGGCCCGCCCCACGGAAGCCCAGCATCg         >  1:796224/1‑143 (MQ=255)

                                                                                                                                cGCACGAACGGGTTCTCGTTCTCAACGTTGGTCAGTCCCCTGTCGTTGCGCACACGTTTCACTGCTTCACCCCCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGtt     <  2:878182/143‑1 (MQ=255)

                                                                                                                                  cgcggccGGGTTCATGCTCTCATCGTTGGTCTGCCCCATGTCGTTGCGCACACGTTTCACTGCTTCACCCTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTtct   <  2:354906/137‑1 (MQ=255)

                                                                                                                                  cACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGAGAGCTGTCGGAAACATAGCGGCCCGCGCCCCGGAAGCCGAGCATCGGGttac   >  2:85525/1‑141 (MQ=255)

                                                                                                                                   aCGAACGGGTTCATGATCTCACCGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTtctc  <  1:799098/143‑1 (MQ=255)

                                                                                                                                   aCGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTtctc  <  2:265248/143‑1 (MQ=255)

GGAACTGCTCGGCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACAGTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTTCTC  >  NC_000913/1785039‑1785312

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A