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	2,584,314	A→G	11.7%	V988A (GTT→GCT)	mdtF ←	multidrug transporter, RpoS‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,584,314	0	A	G	11.7%	270.6 / 23.0	102	V988A (GTT→GCT)	mdtF	multidrug transporter, RpoS‑dependent
Reads supporting (aligned to +/- strand): ref base A (45/45); new base G (5/7); total (50/52)
Fisher's exact test for biased strand distribution p-value = 7.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.43e-01

Only 100 of 103 total aligned reads displayed.

AAACATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGC  >  minE/2584247‑2584384

aaaCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCa                                                                     <  1:772220/71‑1 (MQ=255)

 aaCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAg                                                                    >  1:472032/1‑71 (MQ=255)

  aCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGc                                                                   <  1:277293/71‑1 (MQ=255)

  aCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGc                                                                   <  1:894614/71‑1 (MQ=255)

  aCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGc                                                                   >  1:2160972/1‑71 (MQ=255)

  aCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGc                                                                   >  1:1285875/1‑71 (MQ=255)

   cATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCg                                                                  <  1:430463/71‑1 (MQ=255)

   cATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCg                                                                  <  1:29536/71‑1 (MQ=255)

   cATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCg                                                                  <  1:3067802/71‑1 (MQ=255)

      cccGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATTACTGATAACCAGCgg                                                                 >  1:1515364/1‑69 (MQ=255)

       ccGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                              >  1:1901561/1‑71 (MQ=255)

       ccGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                              <  1:165949/71‑1 (MQ=255)

       ccGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                              <  1:2775054/71‑1 (MQ=255)

             aTCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        <  1:606367/71‑1 (MQ=255)

                aCGCCGTTACGTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        >  1:8647/1‑68 (MQ=255)

                aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCg                                                                  <  1:1922047/58‑1 (MQ=255)

                aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCg                                                                  <  1:1381577/58‑1 (MQ=255)

                aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        >  1:761617/1‑68 (MQ=255)

                aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        >  1:1453642/1‑68 (MQ=255)

                aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        >  1:1972868/1‑68 (MQ=255)

                   ccGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAAt                                                  <  1:2638641/71‑1 (MQ=255)

                    cGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAAt                                                  <  1:389211/70‑1 (MQ=255)

                     gatacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATaa                                                <  1:3682627/69‑1 (MQ=9)

                      gTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                 >  1:2777140/1‑69 (MQ=255)

                      gTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                 >  1:1324176/1‑69 (MQ=255)

                        acctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                >  1:548358/1‑68 (MQ=255)

                        acctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                >  1:1176241/1‑68 (MQ=255)

                          ctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                 <  1:2550853/65‑1 (MQ=255)

                          ctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGc                                            >  1:3605113/1‑70 (MQ=255)

                          ctaccGCGTTTTGCCCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGcc                                           <  1:3879304/71‑1 (MQ=255)

                           taccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGc                                                                   >  1:1163114/1‑46 (MQ=255)

                            accGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                              >  1:1470166/1‑50 (MQ=255)

                            acagcgTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGag                                         <  1:3860792/68‑1 (MQ=9)

                             ccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcagca                                                            >  1:72767/1‑51 (MQ=255)

                             ccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCag                                         <  1:78835/70‑1 (MQ=255)

                              cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                       <  1:2617272/71‑1 (MQ=255)

                              cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                          >  1:1033604/1‑68 (MQ=255)

                              cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                          >  1:825207/1‑68 (MQ=255)

                                 gTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCAc                                                           >  1:458692/1‑48 (MQ=255)

                                 gTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAgg                                    >  1:1638040/1‑71 (MQ=255)

                                 gTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAgg                                    >  1:798087/1‑71 (MQ=255)

                                    ttGCGCGCCAGAACCGGCACCATGCCTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGCGGtca                                 >  1:683703/1‑71 (MQ=255)

                                    ttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAgg                                             >  1:2058887/1‑59 (MQ=255)

                                    ttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAgg                                             >  1:2755116/1‑59 (MQ=255)

                                    ttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCaga                                        >  1:3515077/1‑64 (MQ=255)

                                    ctGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtca                                 >  1:3009935/2‑71 (MQ=255)

                                     tGCGCGCCAGAACCGGCACCATGAGTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtca                                 <  1:449981/70‑1 (MQ=255)

                                      gcgcgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtcat                                <  1:1818497/70‑1 (MQ=255)

                                      gcgcgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtcat                                <  1:2212633/70‑1 (MQ=255)

                                       cgcgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagagag                                     >  1:2061067/1‑64 (MQ=255)

                                         cgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAgg                            <  1:1064270/71‑1 (MQ=255)

                                         cgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAg                             <  1:3726042/70‑1 (MQ=255)

                                         cgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAg                             >  1:778072/1‑70 (MQ=255)

                                          gcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                       <  1:3366805/59‑1 (MQ=255)

                                          gcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                           <  1:2138555/71‑1 (MQ=255)

                                           ccAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAgg                                    <  1:1522864/61‑1 (MQ=255)

                                           ccAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGAt                          <  1:2543743/71‑1 (MQ=255)

                                            cAGAACCGGCACCATGACTGATAACCAGCGgcagca                                                            <  1:2425462/36‑1 (MQ=255)

                                            cAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                               <  1:1447311/49‑1 (MQ=255)

                                             aGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                >  1:2330768/1‑47 (MQ=255)

                                             aGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTg                        >  1:2286118/1‑71 (MQ=255)

                                             aGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTg                        >  1:1199883/1‑71 (MQ=255)

                                              gAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTgg                       >  1:2328731/1‑71 (MQ=255)

                                              gAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTgg                       >  1:806792/1‑71 (MQ=255)

                                              gAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTgg                       >  1:3322800/1‑71 (MQ=255)

                                               aaCCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTg                        <  1:1525240/69‑1 (MQ=255)

                                                gccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCgagaga                                      >  1:880052/2‑54 (MQ=255)

                                                gccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGAta                         >  1:243958/2‑66 (MQ=12)

                                                aCCGGCACCATGACTGATAACCAGCGGCAGCACGCCga                                                      >  1:2378583/1‑38 (MQ=255)

                                                  cGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGt                   <  1:3420762/71‑1 (MQ=255)

                                                  cGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGt                   <  1:1801768/71‑1 (MQ=255)

                                                   ggCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACgca                  <  1:3777631/71‑3 (MQ=9)

                                                    gCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACgca                  >  1:1112377/1‑68 (MQ=9)

                                                    gCACCATGACTGATAACCAGCGGCAGCACGCCgaga                                                    >  1:1350824/1‑36 (MQ=255)

                                                    gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGAtt                         <  1:2733812/63‑1 (MQ=255)

                                                    gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaa                 <  1:1981888/71‑1 (MQ=255)

                                                    gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaa                 <  1:1463295/71‑1 (MQ=255)

                                                    gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaa                 <  1:76557/71‑1 (MQ=255)

                                                    gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                  >  1:1447028/1‑70 (MQ=255)

                                                    gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                  >  1:1854631/1‑70 (MQ=255)

                                                      aCCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAAc               >  1:3143752/1‑71 (MQ=255)

                                                      aCCATGACTGATAACCAGCGGCAGCAAGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaaa                >  1:478243/1‑70 (MQ=255)

                                                        cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGc             <  1:3305821/71‑1 (MQ=255)

                                                         aTGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCa            >  1:1044603/1‑71 (MQ=255)

                                                          ttaCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGgacgcagacgca            >  1:318409/3‑70 (MQ=2)

                                                            aCTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATcc         <  1:2894015/71‑1 (MQ=255)

                                                            aCTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATcc         <  1:2357308/71‑1 (MQ=255)

                                                             cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAggac                     <  1:3151316/58‑3 (MQ=9)

                                                             cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAggac                     <  1:3012318/58‑3 (MQ=9)

                                                             cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAggac                     <  1:263185/58‑3 (MQ=9)

                                                             cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACGCAGACGCAtac         <  1:627934/70‑3 (MQ=9)

                                                             cTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATcc         <  1:35348/70‑1 (MQ=255)

                                                              tGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTgg                       <  1:3715236/55‑1 (MQ=255)

                                                               gATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGAtt                         <  1:2947039/52‑1 (MQ=255)

                                                                aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaaa                >  1:2626189/1‑60 (MQ=255)

                                                                aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCAt           >  1:1428238/1‑65 (MQ=255)

                                                                aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCcgcg      >  1:2795092/1‑70 (MQ=255)

                                                                 tAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCgcgc     <  1:634815/70‑1 (MQ=255)

                                                                 tAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGcgcc    <  1:264338/71‑1 (MQ=255)

                                                                   aCCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGcgccgc  <  1:3082112/71‑1 (MQ=255)

AAACATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGC  >  minE/2584247‑2584384

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