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
A4 F21 I0 R1	1009	73.8	4146436	87.4%	3623985	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,557,415	A→G	25.5%	*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	25.5%	84.2 / 32.2	51	*128Q (TAG→CAG)	emrY	predicted multidrug efflux system
Reads supporting (aligned to +/- strand): ref base A (22/16); new base G (8/5); total (30/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

ACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTG  >  minE/1557345‑1557485

aCGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTa                                                                        >  1:556037/1‑71 (MQ=255)

  ggTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATg                                                                      <  1:241780/71‑1 (MQ=255)

    tCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGAc                                                                    <  1:3181354/71‑1 (MQ=255)

      aTTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAg                                                                  >  1:4016008/1‑71 (MQ=255)

      aTTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGAc                                                                    <  1:318410/69‑1 (MQ=255)

          aCCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTgg                                                               <  1:2706555/70‑1 (MQ=255)

             aTAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGa                                                                     >  1:2311970/1‑61 (MQ=255)

             aTAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAAtt                                                           <  1:1532109/71‑1 (MQ=255)

             aTAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAAtt                                                           <  1:2928401/71‑1 (MQ=255)

              tAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTa                                                          <  1:1690163/71‑1 (MQ=255)

                aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTaa                                                         <  1:1501251/70‑1 (MQ=255)

                aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTaa                                                         <  1:2180087/70‑1 (MQ=255)

                aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTaa                                                         <  1:2886753/70‑1 (MQ=255)

                 tGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACg                                                       <  1:1030696/71‑1 (MQ=255)

                     agagCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGccc                                                   >  1:3954368/1‑71 (MQ=255)

                        gCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGc                                                >  1:2402913/1‑71 (MQ=255)

                         cAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAAtt                                                           <  1:3623722/59‑1 (MQ=255)

                           aaTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATg                                                                      >  1:600935/1‑46 (MQ=255)

                           aaTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTaa                                                         >  1:2286974/1‑59 (MQ=255)

                           aaTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACg                                                       >  1:4016292/1‑61 (MQ=255)

                           aaTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCAt                                             >  1:3698717/1‑71 (MQ=255)

                            aTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTaa                                                         >  1:366650/1‑58 (MQ=255)

                             tGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTAt                                                                       <  1:2004271/43‑1 (MQ=255)

                               ttCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAAc                                         >  1:1611653/1‑71 (MQ=255)

                                tCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACATTGGa                                                              >  1:1600813/1‑49 (MQ=255)

                                tCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAAtt                                                           <  1:4021655/52‑1 (MQ=255)

                                  ttttttCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAAcccc                                      >  1:1747362/1‑71 (MQ=255)

                                   tttttCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTaa                                                         <  1:1950407/51‑1 (MQ=255)

                                    ttttCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAg                                                                  >  1:2982843/1‑41 (MQ=255)

                                    ttttCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCt                                     >  1:623633/1‑70 (MQ=255)

                                    ttttCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCt                                     >  1:1908504/1‑70 (MQ=255)

                                     tttCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCt                                     >  1:1108291/1‑69 (MQ=255)

                                            cGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGActc                            >  1:2175702/1‑71 (MQ=255)

                                                tAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaa                         >  1:1866499/1‑70 (MQ=255)

                                                tAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGcccc                                                  >  1:155182/1‑45 (MQ=255)

                                                 aaTTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaa                        >  1:302238/1‑70 (MQ=255)

                                                  aTTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaaa                       <  1:3900222/70‑1 (MQ=255)

                                                   ttCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGc                                                <  1:3674928/44‑1 (MQ=255)

                                                   ttCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaagaa                     >  1:3977819/1‑71 (MQ=255)

                                                     ccTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAat                    <  1:311602/70‑1 (MQ=255)

                                                      cTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAata                   <  1:2945266/70‑1 (MQ=255)

                                                             ataaACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGcaca           >  1:583039/1‑71 (MQ=255)

                                                             ataaACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATc                 >  1:833182/1‑65 (MQ=255)

                                                                aaCTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATc         >  1:2145547/1‑70 (MQ=255)

                                                                aaCTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATc         >  1:3581191/1‑70 (MQ=255)

                                                                aaCTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATc         >  1:1873580/1‑70 (MQ=255)

                                                                 aCTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATc         >  1:3810162/1‑69 (MQ=255)

                                                                 aCTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCaa       <  1:3495064/71‑1 (MQ=255)

                                                                  ctctATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATc         >  1:3518328/1‑68 (MQ=255)

                                                                   tctATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaaa                       <  1:3232609/53‑1 (MQ=255)

                                                                     tATGACAGTGGAATTAACGGCCCCGCCATTACCCCCTGAACGACTCTAAAAAATATCAGCACATCAAGAtt   >  1:2597682/1‑71 (MQ=255)

                                                                     tATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGAtt   >  1:3259004/1‑71 (MQ=255)

                                                                      aTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTg  >  1:1926482/1‑71 (MQ=255)

ACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTG  >  minE/1557345‑1557485

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