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	2,298,218	T→A	36.6%	intergenic (‑148/+181)	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	2,298,218	0	T	A	36.6%	108.8 / 113.1	131	intergenic (‑148/+181)	katG/metF	catalase/hydroperoxidase HPI(I)/5,10‑methylenetetrahydrofolate reductase
Reads supporting (aligned to +/- strand): ref base T (41/42); new base A (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 137 total aligned reads displayed.

AGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATCCTTCAAGT  >  minE/2298154‑2298282

aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCATATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:2624631/69‑1 (MQ=255)

aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:3029174/69‑1 (MQ=255)

aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:1862388/69‑1 (MQ=255)

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

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

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

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

aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:3235491/69‑1 (MQ=255)

aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:3396328/69‑1 (MQ=255)

aGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGAt                                                              <  1:822804/69‑1 (MQ=255)

   tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:3190083/69‑1 (MQ=255)

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

   tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:1095968/69‑1 (MQ=255)

   tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:2697023/69‑1 (MQ=255)

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

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

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

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

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

   tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:622482/69‑1 (MQ=255)

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

   tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:1225697/69‑1 (MQ=255)

   tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:1201120/69‑1 (MQ=255)

   tGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:112474/69‑1 (MQ=255)

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

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

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

    gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:566503/1‑64 (MQ=255)

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

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

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

    gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:2917337/1‑64 (MQ=255)

    gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:3311706/1‑64 (MQ=255)

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

    gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:2992267/1‑64 (MQ=255)

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

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

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

    gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:3168352/1‑64 (MQ=255)

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

    gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGagt                                                             >  1:1878568/1‑64 (MQ=255)

    gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGag                                                              >  1:316266/1‑64 (MQ=255)

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

    gagaTCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCGTAATTAAGCCTTTATGAGTAt                                                           <  1:2137129/68‑1 (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                                              >  1:3000015/1‑68 (MQ=255)

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

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

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

                 ttgttgGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGa                                              >  1:346897/1‑68 (MQ=255)

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

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

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

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

                                     gATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:43736/1‑50 (MQ=255)

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

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

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

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

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

                                        cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:3316227/1‑47 (MQ=255)

                                        cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:358403/1‑47 (MQ=255)

                                        cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:1756882/1‑47 (MQ=255)

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

                                        cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACa                                            >  1:1683915/1‑47 (MQ=255)

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

                                        cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAggga                        >  1:2254293/1‑66 (MQ=255)

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

                                        cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:786144/1‑67 (MQ=255)

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

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

                                        cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:710397/1‑67 (MQ=255)

                                        cAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGt                        >  1:2604949/1‑67 (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                     <  1:1271510/69‑1 (MQ=255)

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

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

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

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

                                                 cTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCa              <  1:2059346/68‑1 (MQ=255)

                                                 cTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCa              <  1:1426407/68‑1 (MQ=255)

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

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

                                                      ttaaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATc          <  1:847464/67‑1 (MQ=255)

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

                                                      ttaaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATc          <  1:212810/67‑1 (MQ=255)

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

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

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

                                                       taaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:1990051/64‑1 (MQ=255)

                                                       taaGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCata            <  1:523343/64‑1 (MQ=255)

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

                                                            ttttttGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATCCTTCAAGt  <  1:2946321/69‑1 (MQ=255)

                                                            ttttttGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATCCTTCAAGt  <  1:1630701/69‑1 (MQ=255)

                                                            ttttttGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATCCTTCAAGt  <  1:2340633/69‑1 (MQ=255)

AGTTGAGATCTTACATATTGTTGGTTAAAGAGATGTAGATCAAATTGATCTTAATTAAGCTTTTTTGATTATGTCCGAATTCGGACAAATGCTTTATAAAAAAGGGTTTTAGCTTCATATCCTTCAAGT  >  minE/2298154‑2298282

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