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
A1 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,589,664	A→T	80.3%	intergenic (+300/‑239)	acrD → / → yffB	aminoglycoside/multidrug efflux system/conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,589,664	0	A	T	80.3%	150.4 / 32.1	66	intergenic (+300/‑239)	acrD/yffB	aminoglycoside/multidrug efflux system/conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (7/6); new base T (33/20); total (40/26)
Fisher's exact test for biased strand distribution p-value = 7.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

ACTACCTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTAAAATACAGA  >  W3110S.gb/2589602‑2589731

aCTACCTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAg                                                              >  1:2368000/1‑70 (MQ=255)

aCTACCTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAg                                                              >  1:3542696/1‑70 (MQ=255)

aCTACCTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAg                                                              >  1:2325382/1‑70 (MQ=255)

aCTACCTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAg                                                              >  1:3042459/1‑70 (MQ=255)

    ccTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           <  1:2606134/69‑1 (MQ=255)

    ccTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           <  1:1881317/69‑1 (MQ=255)

    ccTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACa                                                         >  1:3095898/1‑71 (MQ=255)

            ggACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCgaga                                                 <  1:2882100/71‑1 (MQ=255)

                aaaTCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAGCAACATTTCGAGATAtt                                             <  1:391156/71‑1 (MQ=255)

                aaaTCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAGCAACATTTCGAGATAtt                                             <  1:2358758/71‑1 (MQ=255)

                aaaTCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAGCAACATTTCGAGATAtt                                             <  1:1663401/71‑1 (MQ=255)

                   tCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAGCAACATTTCga                                                   <  1:1174713/62‑1 (MQ=255)

                   tCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAGCAACATTTCga                                                   <  1:2050465/62‑1 (MQ=255)

                    cTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:2381695/1‑65 (MQ=255)

                    cTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:1949956/1‑65 (MQ=255)

                          tAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCgaga                                                 <  1:2328212/57‑1 (MQ=255)

                          tAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:768279/1‑59 (MQ=255)

                          tAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:3019542/1‑59 (MQ=255)

                          tAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:2178070/1‑59 (MQ=255)

                          tAAATACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCa                                    <  1:835798/70‑1 (MQ=255)

                            aaTACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCgaga                                                 <  1:1669104/55‑1 (MQ=255)

                            aaTACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCt                                 <  1:337880/71‑1 (MQ=255)

                            aaTACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCt                                 <  1:997359/71‑1 (MQ=255)

                              tACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:2560158/1‑55 (MQ=255)

                              tACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:3098046/1‑55 (MQ=255)

                              tACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:2517420/1‑55 (MQ=255)

                              tACTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGata                                               >  1:39875/1‑55 (MQ=255)

                               aCTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           >  1:97469/1‑42 (MQ=255)

                               aCTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           >  1:576877/1‑42 (MQ=255)

                               aCTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           >  1:2522356/1‑42 (MQ=255)

                               aCTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           >  1:3493176/1‑42 (MQ=255)

                               aCTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           >  1:3319414/1‑42 (MQ=255)

                               aCTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           >  1:3291527/1‑42 (MQ=255)

                               aCTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           >  1:1364111/1‑42 (MQ=255)

                               aCTATGCTCCTGCGGTGATGATTTGTATGTGTTACACAGCaa                                                           >  1:3487625/1‑42 (MQ=38)

                                cTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCa                                                            >  1:2042559/1‑40 (MQ=255)

                                cTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTaa                               >  1:109103/1‑69 (MQ=255)

                                cTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTaa                               >  1:1323908/1‑69 (MQ=255)

                                cTATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTaa                               >  1:2758331/1‑69 (MQ=255)

                                 tATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAAc                                                          <  1:1240612/41‑1 (MQ=255)

                                 tATGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAAc                                                          <  1:673484/41‑1 (MQ=255)

                                  aTGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCa                                           >  1:2346594/1‑55 (MQ=255)

                                  aTGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCa                                           >  1:164213/1‑55 (MQ=255)

                                  aTGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCa                                           >  1:1594932/1‑55 (MQ=255)

                                  aTGGTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCa                                           >  1:3424049/1‑55 (MQ=255)

                                    ggTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCa                                           >  1:3173303/1‑53 (MQ=255)

                                    ggTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCa                                           >  1:595270/1‑53 (MQ=255)

                                    ggTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCa                                           >  1:2331596/1‑53 (MQ=255)

                                    ggTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTg                          <  1:3547235/70‑1 (MQ=255)

                                     gTCCTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGAt                        >  1:226161/1‑71 (MQ=255)

                                       ccTGCGGTGATGATTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGAtt                       >  1:1336348/1‑70 (MQ=255)

                                        cTGCGGTGATGATTTGTATGTGATACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTa                     <  1:2504301/71‑1 (MQ=255)

                                              tgatgaTTTGTATGTGTTACACAGCAACATTTCgaga                                                 <  1:3537594/37‑1 (MQ=255)

                                                   atTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTaa          <  1:252956/71‑1 (MQ=255)

                                                   atTTGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTaa          <  1:1146934/71‑1 (MQ=255)

                                                   atTTGTATGTGATACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTa           >  1:1047405/1‑70 (MQ=255)

                                                      tGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTaaaa        <  1:1359382/70‑1 (MQ=255)

                                                      tGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTaaaa        <  1:597441/70‑1 (MQ=255)

                                                      tGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTaaaa        <  1:2669203/70‑1 (MQ=255)

                                                      tGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTaaaa        <  1:3032543/70‑1 (MQ=255)

                                                      tGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTaaaa        <  1:804593/70‑1 (MQ=255)

                                                      tGTATGTGTTACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTaaaa        <  1:2001652/70‑1 (MQ=255)

                                                             gATACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTAAAATacaga  >  1:2814700/1‑69 (MQ=255)

                                                             gATACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTAAAATacaga  >  1:2539442/1‑69 (MQ=255)

                                                             gATACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTAAAATacaga  >  1:1293751/1‑69 (MQ=255)

                                                             gATACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTAAAATacaga  >  1:955520/1‑69 (MQ=255)

ACTACCTCCGGGGGACAAATCTTATGTAAATACTATGGTCCTGCGGTGATGATTTGTATGTGATACACAGCAACATTTCGAGATATTCATACGGCATCTAATACTGATTTAATTCTGGTTAAAATACAGA  >  W3110S.gb/2589602‑2589731

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A