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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,558,525	C→T	37.2%	Q145Q (CAG→CAA)	emrK ←	EmrKY‑TolC multidrug resistance efflux pump, membrane fusion protein component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,558,525	0	C	T	37.2%	32.0 / 35.1	59	Q145Q (CAG→CAA)	emrK	EmrKY‑TolC multidrug resistance efflux pump, membrane fusion protein component
Reads supporting (aligned to +/- strand): ref base C (26/11); new base T (15/7); total (41/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.66e-01

CAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATA  >  minE/1558459‑1558582

cAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTg                                                         >  1:1286397/1‑69 (MQ=255)

cAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTg                                                         >  1:983448/1‑69 (MQ=255)

cAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTg                                                         >  1:552348/1‑69 (MQ=255)

cAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTg                                                         >  1:2677321/1‑69 (MQ=255)

cAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTg                                                         >  1:1868670/1‑69 (MQ=255)

cAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTg                                                         >  1:185161/1‑69 (MQ=255)

cAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTg                                                         >  1:1643350/1‑69 (MQ=255)

    gCCGCTTTTCTACTTATTAACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTc                                                     >  1:2027565/1‑69 (MQ=255)

    gCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCtt                                                      >  1:2661004/1‑68 (MQ=255)

    gCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTc                                                     >  1:2161306/1‑69 (MQ=255)

    gCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTc                                                     >  1:940789/1‑69 (MQ=255)

    gCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTc                                                     >  1:837680/1‑69 (MQ=255)

    gCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTc                                                     >  1:3126635/1‑69 (MQ=255)

    gCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTc                                                     >  1:59070/1‑69 (MQ=255)

    gCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTc                                                     >  1:2464033/1‑69 (MQ=255)

    gCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTc                                                     >  1:1517317/1‑69 (MQ=255)

    gCCGCTATGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTc                                                     >  1:442071/1‑69 (MQ=255)

       gCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCt                                                  <  1:3004834/69‑1 (MQ=255)

       gCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCt                                                  <  1:2903579/69‑1 (MQ=255)

               aCTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCa                                           <  1:3420410/68‑1 (MQ=255)

               aCTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCa                                           <  1:2926422/68‑1 (MQ=255)

               aCTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCa                                           <  1:2385677/68‑1 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTc                                        <  1:137985/68‑1 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTc                                        <  1:2603351/68‑1 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCAcac                                        <  1:1673087/68‑3 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCAcac                                        <  1:1329654/68‑3 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCAcac                                        <  1:2925479/68‑3 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCAcac                                        <  1:2532172/68‑3 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCAcac                                        <  1:593801/68‑3 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCAcac                                        <  1:1861090/68‑3 (MQ=255)

                  tattaACGTATCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCAcac                                        <  1:2226633/68‑3 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACgg                                             >  1:2411394/1‑59 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACgg                                             >  1:2688921/1‑59 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACgg                                             >  1:979809/1‑59 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACgg                                             >  1:3084039/1‑59 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACgg                                             >  1:3087051/1‑59 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACgg                                             >  1:3153439/1‑59 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACgg                                             >  1:1530326/1‑59 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACg                                    >  1:2304429/1‑68 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACg                                    >  1:1843721/1‑68 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACg                                    >  1:1646379/1‑68 (MQ=255)

                      aaCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACg                                    >  1:1839692/1‑68 (MQ=255)

                           aTCTTTGGTATGCTCCAGGGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCACACGACGGTtata                              >  1:304207/1‑69 (MQ=255)

                           aTCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGc                                            >  1:1863320/1‑55 (MQ=255)

                           aTCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCACACGATGGTtat                               >  1:1660258/1‑68 (MQ=255)

                           aTCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCACACGACGGTtata                              >  1:2379192/1‑69 (MQ=255)

                           aTCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCACACGACGGTtat                               >  1:641910/1‑68 (MQ=255)

                           aTCTTTGGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCACACGACGGTtat                               >  1:794306/1‑68 (MQ=255)

                           aTCTTTCGTATGCTCCAGCGCTTCTTTTGAAATAACCCCTTGCTTCGCTAAAGGCACACGACGGTtat                               >  1:438027/1‑68 (MQ=255)

                                       cTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAg                   <  1:884130/68‑1 (MQ=255)

                                       cTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAg                   <  1:2246930/68‑1 (MQ=255)

                                       cTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGa                  >  1:10865/1‑69 (MQ=255)

                                       cTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGa                  >  1:428407/1‑69 (MQ=255)

                                       cTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGa                  >  1:2415576/1‑69 (MQ=255)

                                       cTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGa                  >  1:164577/1‑69 (MQ=255)

                                                 tCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATa         >  1:540173/1‑68 (MQ=255)

                                                 tCTTTTGAAATAACCCCCTGCTTCGCTAACGCCACTCGACGGTTATAATCTTCTAAAGATTGTTGATa         >  1:2277848/1‑68 (MQ=255)

                                                        aaaTAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATa  <  1:865928/68‑1 (MQ=255)

                                                        aaaTAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATa  <  1:2566742/68‑1 (MQ=255)

CAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATA  >  minE/1558459‑1558582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A