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	2,298,214	T→C	36.9%	intergenic (‑144/+185)	katG ← / ← metF	catalase/hydroperoxidase HPI(I)/5,10‑methylenetetrahydrofolate reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,298,214	0	T	C	36.9%	76.0 / 83.5	131	intergenic (‑144/+185)	katG/metF	catalase/hydroperoxidase HPI(I)/5,10‑methylenetetrahydrofolate reductase
Reads supporting (aligned to +/- strand): ref base T (40/42); new base C (19/29); total (60/71)
Fisher's exact test for biased strand distribution p-value = 3.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 163 total aligned reads displayed.

GCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATCCTTCAAGT  >  minE/2298149‑2298282

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:372846/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:318729/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:3154614/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:3302755/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:1712005/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:2795414/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:1383082/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:2782432/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:2718216/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:2676439/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:1208436/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:579670/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:2624113/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:1107834/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:1089294/1‑69 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCctt                                                                    >  1:356264/1‑68 (MQ=255)

gCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCctt                                                                    >  1:1648566/1‑68 (MQ=255)

     aGTTGAGATCTTACATATTGTTGGTTAAAGATATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:3235029/69‑1 (MQ=255)

     aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:2891621/69‑1 (MQ=255)

     aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:139534/69‑1 (MQ=255)

     aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:211519/69‑1 (MQ=255)

     aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:2321585/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTaa                                                           <  1:476622/69‑2 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:1092003/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:3364369/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:2971882/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:2917673/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:426738/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:54896/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:586713/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:249051/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:2279824/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:220262/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:1710773/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:1790055/69‑1 (MQ=255)

        tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATAGTAATTAAGCCTTTATGAGTAt                                                           <  1:2930690/69‑1 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCcttt                                                                   >  1:3326437/1‑60 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:1683105/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:2276898/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:3181340/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:3150091/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:3252759/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:78054/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:2432000/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:291317/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:1943851/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:1682841/68‑1 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:2137129/68‑1 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:2121641/68‑1 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGACTTTATGagt                                                             >  1:1934716/1‑64 (MQ=255)

         gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGACTTTATGAGTAt                                                           <  1:3377873/68‑1 (MQ=255)

                      ttgttgGTTAAAGAGATGTAGATCAAATTGCTCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGa                                              >  1:2338671/1‑68 (MQ=255)

                      ttgttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGa                                                               >  1:1994821/1‑51 (MQ=255)

                      ttgttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGa                                              >  1:352791/1‑68 (MQ=255)

                      ttgttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGa                                              >  1:794380/1‑68 (MQ=255)

                      ttgttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGa                                              >  1:2401551/1‑68 (MQ=255)

                      ttgttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGa                                              >  1:2999104/1‑68 (MQ=255)

                      ttgttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGa                                              >  1:3000015/1‑68 (MQ=255)

                        gttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCt                                                                      >  1:1122620/1‑42 (MQ=255)

                        gttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACaa                                           >  1:838569/1‑69 (MQ=255)

                        gttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            <  1:1142379/68‑1 (MQ=255)

                                          gATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:3165434/1‑50 (MQ=255)

                                          gATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:516741/1‑50 (MQ=255)

                                          gATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:192198/1‑50 (MQ=255)

                                          gATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAggg                         <  1:2825345/69‑1 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:76882/1‑47 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:3312150/1‑47 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:757653/1‑47 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:732005/1‑47 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:984291/1‑47 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:2400047/1‑47 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:2237427/1‑47 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:2604949/1‑67 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:3313620/1‑67 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:2675150/1‑67 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:878502/1‑67 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:1269840/1‑67 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:1360141/1‑67 (MQ=255)

                                             cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGCGt                        >  1:1635373/1‑67 (MQ=255)

                                             cAAATTGATCTTAATTAAG‑ATTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGtttt                     >  1:3098031/1‑69 (MQ=255)

                                              aaaTTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGtttt                     <  1:1323962/69‑1 (MQ=255)

                                              aaaTTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGtttt                     <  1:3012876/69‑1 (MQ=255)

                                               aaTTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGtttt                     <  1:3048772/68‑1 (MQ=255)

                                                 ttGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGtttt                     <  1:39891/66‑1 (MQ=255)

                                                      cTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCa              <  1:2394484/68‑1 (MQ=255)

                                                      cTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCa              <  1:2638267/68‑1 (MQ=255)

                                                      cTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCa              <  1:73586/68‑1 (MQ=255)

                                                      cTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCa              <  1:2022597/68‑1 (MQ=255)

                                                           ttaaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:890507/65‑1 (MQ=255)

                                                           ttaaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:3425265/65‑1 (MQ=255)

                                                           ttaaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:176778/65‑1 (MQ=255)

                                                           ttaaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:666983/65‑1 (MQ=255)

                                                           ttaaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATc          <  1:1672565/67‑1 (MQ=255)

                                                           ttaaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGATTTAGCTTCata            <  1:2263095/65‑1 (MQ=255)

                                                            taaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:1211386/64‑1 (MQ=255)

                                                            taaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:1871385/64‑1 (MQ=255)

                                                            taaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:1628507/64‑1 (MQ=255)

                                                            taaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:180766/64‑1 (MQ=255)

                                                             aaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATcc         >  1:2485180/1‑66 (MQ=255)

                                                                 ttttttGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATCCTTCAAGt  <  1:809469/69‑1 (MQ=255)

GCGATAGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATCCTTCAAGT  >  minE/2298149‑2298282

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