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 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	982,632	A→C	31.6%	A26A (GCA→GCC)	ydfA →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	982,632	0	A	C	31.6%	137.7 / 142.4	152	A26A (GCA→GCC)	ydfA	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (43/61); new base C (19/29); total (62/90)
Fisher's exact test for biased strand distribution p-value = 8.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 158 total aligned reads displayed.

ATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACT  >  minE/982564‑982699

 tCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAAt                                                                   >  1:2985504/1‑70 (MQ=255)

 tCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAAt                                                                   >  1:5238324/1‑70 (MQ=255)

  cGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATg                                                                  >  1:2933886/1‑70 (MQ=255)

  cGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGa                                                                 >  1:1089754/1‑71 (MQ=255)

  cGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGa                                                                 >  1:3132958/1‑71 (MQ=255)

   gATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGAc                                                                >  1:1627117/1‑71 (MQ=255)

      ctcggCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACg                                                               <  1:2015484/66‑1 (MQ=255)

      ctcggCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACg                                                               <  1:3665795/66‑1 (MQ=255)

      cTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                             >  1:4769378/1‑71 (MQ=255)

      cTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                             >  1:4194718/1‑71 (MQ=255)

      cTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                             >  1:2658389/1‑71 (MQ=255)

      cTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                             >  1:3541868/1‑71 (MQ=255)

      cTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                             >  1:1714743/1‑71 (MQ=255)

        tGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGtata                                                           >  1:4917035/1‑71 (MQ=255)

        cggCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGa                                                                 >  1:2261816/2‑65 (MQ=255)

         ggCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCAGGTTCACCGCAATGACGTATAc                                                          >  1:5165757/1‑71 (MQ=255)

         ggCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACg                                                               <  1:5432214/66‑1 (MQ=255)

          gCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                             <  1:1698663/67‑1 (MQ=255)

          gCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATAcc                                                         <  1:4958940/71‑1 (MQ=255)

           caacaaCGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATAcc                                                         >  1:4368369/1‑70 (MQ=255)

            aacaacGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCaa                                                       <  1:5425847/71‑1 (MQ=255)

            aacaacGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCaa                                                       <  1:4636744/71‑1 (MQ=255)

            aacaacGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCaa                                                       <  1:587474/71‑1 (MQ=255)

            aacaacGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCaa                                                       <  1:5612030/71‑1 (MQ=255)

             acaacGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCaaa                                                      <  1:3543836/71‑1 (MQ=255)

               aacGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCa                                                                     <  1:2332322/54‑1 (MQ=255)

                  gAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaa                                                 <  1:3691746/71‑1 (MQ=255)

                  gAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaa                                                 <  1:147057/71‑1 (MQ=255)

                    aTCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCaaaa                                               <  1:5534185/71‑1 (MQ=255)

                    aTCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCaaaa                                               <  1:4875973/71‑1 (MQ=255)

                     tccctGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCaa                                                 <  1:1763209/65‑1 (MQ=255)

                      ctctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaa                                                >  1:2412398/1‑68 (MQ=255)

                      ctctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaa                                                >  1:2656630/1‑68 (MQ=255)

                      ctctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaa                                                >  1:1740954/1‑68 (MQ=255)

                       tctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGtata                                                           >  1:1169894/1‑56 (MQ=255)

                         tGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACg                                             <  1:3554955/68‑1 (MQ=255)

                           gtgtGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                                          <  1:2964101/69‑1 (MQ=255)

                           gtgtGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaa                                        <  1:5040189/71‑1 (MQ=255)

                           gtgtGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTa                                         <  1:312039/70‑1 (MQ=255)

                           gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaa                                        <  1:4165288/71‑1 (MQ=255)

                           gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaa                                        <  1:3155242/71‑1 (MQ=255)

                           gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTa                                         >  1:5248812/1‑70 (MQ=255)

                           gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTa                                         <  1:5164881/70‑1 (MQ=255)

                            tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                                       <  1:3289837/71‑1 (MQ=255)

                            tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                                       <  1:718535/71‑1 (MQ=255)

                            tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaa                                        >  1:1653029/1‑70 (MQ=255)

                            tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaa                                        >  1:157976/1‑70 (MQ=255)

                            tgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaaa                                       <  1:5295608/71‑1 (MQ=255)

                              tACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACg                                                               <  1:3186065/45‑1 (MQ=255)

                                cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCaa                                                                    >  1:3903751/1‑38 (MQ=255)

                                cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCaa                                                                    >  1:477412/1‑38 (MQ=255)

                                cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCg                                   <  1:2057759/71‑1 (MQ=255)

                                cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCg                                   <  1:2442740/71‑1 (MQ=255)

                                cGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCg                                   <  1:2175992/71‑1 (MQ=255)

                                 ggCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACg                                                               <  1:2238668/42‑1 (MQ=255)

                                 ggCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACg                                                               <  1:3771331/42‑1 (MQ=255)

                                   cGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaaa                                <  1:1957919/71‑1 (MQ=255)

                                   cGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                >  1:2098552/1‑71 (MQ=255)

                                     tgtTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGt                                            <  1:3731539/57‑1 (MQ=255)

                                     tgtTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGt                                            <  1:3591019/57‑1 (MQ=255)

                                       tttCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGttt                                          >  1:4496144/1‑57 (MQ=255)

                                         tCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                             >  1:5614570/1‑36 (MQ=255)

                                         tCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                             >  1:1068631/1‑36 (MQ=255)

                                           cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaaa                                               >  1:1941308/1‑48 (MQ=255)

                                           cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGcc                        >  1:5012760/1‑71 (MQ=255)

                                           cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGcc                        >  1:4718072/1‑71 (MQ=255)

                                           cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGc                         <  1:1448562/70‑1 (MQ=255)

                                            caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                                          >  1:5544429/2‑52 (MQ=255)

                                            caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                                          >  1:3571703/2‑52 (MQ=255)

                                            caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                                          >  1:1347487/2‑52 (MQ=255)

                                            caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                                          >  1:2897144/2‑52 (MQ=255)

                                             aaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGcgcg                      <  1:4637559/71‑1 (MQ=255)

                                             aaCCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACg                                             <  1:2747890/48‑1 (MQ=255)

                                             aaCCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCg                      >  1:4722547/1‑71 (MQ=255)

                                                cAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAAca                                             <  1:1400611/45‑2 (MQ=25)

                                                 aGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGCGCGCCga                  <  1:3247907/71‑2 (MQ=255)

                                                 aGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGCGCGCCga                  <  1:3936469/71‑2 (MQ=255)

                                                 aGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                 <  1:4531709/56‑1 (MQ=255)

                                                   gACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaaa                                               >  1:4873118/1‑40 (MQ=255)

                                                   gACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaaa                                               >  1:2560055/1‑40 (MQ=255)

                                                   gACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                 <  1:667521/54‑1 (MQ=255)

                                                     cGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaaaa                               >  1:4481924/1‑54 (MQ=255)

                                                     cGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATg                             >  1:670407/1‑56 (MQ=255)

                                                        cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                 <  1:131105/49‑1 (MQ=255)

                                                        cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAAt                              <  1:724862/52‑1 (MQ=255)

                                                        cACGTTCACCACAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                 <  1:4415941/49‑1 (MQ=255)

                                                         aCGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                 <  1:3474791/48‑1 (MQ=255)

                                                         aCGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                 <  1:1992832/48‑1 (MQ=255)

                                                            ttCACTGCCATGACGTATACCAAAAGCAAAACAtt                                           <  1:4011734/35‑1 (MQ=25)

                                                            ttCACTGCCATGACGTATACCAAAAGCAAAACAtt                                           <  1:3068998/35‑1 (MQ=25)

                                                             tCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                >  1:3966570/1‑45 (MQ=38)

                                                             tCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                >  1:3860180/1‑45 (MQ=38)

                                                              cACCGCAATGACGTATACCAAAAGCAAAACTTTTAAAAcc                                    <  1:5110408/40‑1 (MQ=255)

                                                              cACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaaga      <  1:2573547/70‑1 (MQ=255)

                                                              cACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaaga      <  1:4180364/70‑1 (MQ=255)

                                                              cACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaaga      <  1:4847846/70‑1 (MQ=255)

                                                               aCCGCAATGACGTATACCAAAAGCAAAACGTTTaaaa                                      >  1:838545/1‑37 (MQ=255)

                                                               aCCGCAATGACGTATACCAAAAGCAAAACGTTTaa                                        <  1:1145679/35‑1 (MQ=255)

                                                                 ctcAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACt  >  1:2670830/3‑71 (MQ=255)

                                                                 cGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTg                          <  1:3073809/47‑1 (MQ=255)

ATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACT  >  minE/982564‑982699

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