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	1,557,415	A→G	68.0%	*128Q (TAG→CAG)	emrY ←	predicted multidrug efflux system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,557,415	0	A	G	68.0%	57.7 / 36.4	50	*128Q (TAG→CAG)	emrY	predicted multidrug efflux system
Reads supporting (aligned to +/- strand): ref base A (8/8); new base G (22/12); total (30/20)
Fisher's exact test for biased strand distribution p-value = 3.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

ACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATC  >  minE/1557345‑1557478

aCGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTa                                                                 >  1:4010411/1‑71 (MQ=255)

   gTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGa                                                              <  1:532485/71‑1 (MQ=255)

   gTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGa                                                              <  1:281719/71‑1 (MQ=255)

      aTTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACa                                                            <  1:3652577/70‑1 (MQ=255)

      aTTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAg                                                           >  1:5636411/1‑71 (MQ=255)

         gACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTg                                                         >  1:5593852/1‑70 (MQ=255)

         gACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTg                                                         >  1:5582545/1‑70 (MQ=255)

         gACAATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTg                                                         >  1:3021763/1‑70 (MQ=255)

          aCCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAg                                                           >  1:4219798/1‑67 (MQ=255)

          aCCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAg                                                           >  1:2217292/1‑67 (MQ=255)

             aTAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAAtt                                                    <  1:4840121/71‑1 (MQ=255)

             aTAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAAtt                                                    <  1:3521445/71‑1 (MQ=255)

              tAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAAtt                                                    >  1:1684411/1‑70 (MQ=255)

              tAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAAtt                                                    >  1:4750502/1‑70 (MQ=255)

              tAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTa                                                   <  1:1578709/71‑1 (MQ=255)

                aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGATTTaaa                                                 <  1:1050019/71‑2 (MQ=255)

                aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTa                                                   <  1:522334/69‑1 (MQ=255)

                aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAAc                                                 >  1:589977/1‑71 (MQ=255)

                aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAAc                                                 >  1:2629875/1‑71 (MQ=255)

                    cAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGcc                                             <  1:2542029/71‑1 (MQ=255)

                        gCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGc                                         >  1:1518878/1‑71 (MQ=255)

                         cAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGt                                                          >  1:4843957/1‑53 (MQ=255)

                         cAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGc                                         >  1:43634/1‑70 (MQ=255)

                           aaTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTg                                                         >  1:1784938/1‑52 (MQ=255)

                           aaTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTg                                                         >  1:3664139/1‑52 (MQ=255)

                              gTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAAc                                                 >  1:4130298/1‑57 (MQ=255)

                              gTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAAc                                                 >  1:4271057/1‑57 (MQ=255)

                                 cTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGaa                                                      >  1:4612182/1‑49 (MQ=255)

                                 cTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACgg                                               >  1:4353994/1‑56 (MQ=255)

                                 cTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGc                                              >  1:1861175/1‑57 (MQ=255)

                                   tttttCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTaa                                   >  1:1489878/1‑66 (MQ=255)

                                   tttttCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTaa                                   >  1:3351831/1‑66 (MQ=255)

                                   tttttCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTaa                                   >  1:435789/1‑66 (MQ=255)

                                    ttttCTGGCGGATAATTCCTTAATAATAAACTCTGTGa                                                              >  1:1015709/1‑38 (MQ=255)

                                    ttttCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCt                              >  1:5680683/1‑70 (MQ=255)

                                     tttCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTg                             <  1:2907756/70‑1 (MQ=255)

                                      ttCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTg                             <  1:5567872/69‑1 (MQ=255)

                                           gCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGa                        <  1:1378334/69‑1 (MQ=255)

                                           gCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGAct                      <  1:4344402/71‑1 (MQ=255)

                                                tAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaa                 <  1:851261/71‑1 (MQ=255)

                                                tAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaa                  >  1:5280095/1‑70 (MQ=255)

                                                tAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaa                  <  1:3882361/70‑1 (MQ=255)

                                                tAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaa                  >  1:4494681/1‑70 (MQ=255)

                                                     ccTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAat             <  1:4427080/70‑1 (MQ=255)

                                                        taataataaACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaaaa               <  1:4174782/65‑1 (MQ=255)

                                                           taataaACTCTGTGACAGTGGAATTAACGGCCCCGCCAtt                                     <  1:2893998/40‑1 (MQ=255)

                                                           taataaACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTg                             <  1:2008252/48‑1 (MQ=255)

                                                             ataaACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGcac     <  1:297822/70‑1 (MQ=255)

                                                               aaaCTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACAt   >  1:5045410/1‑70 (MQ=255)

                                                                aaCTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATc  >  1:218612/1‑70 (MQ=255)

                                                                aaCTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATc  >  1:2203406/1‑70 (MQ=255)

ACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATC  >  minE/1557345‑1557478

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