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 F50 I1 R1	14	46.8	1456587	99.0%	1442021	150.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,182,583	C→T	H447Y (CAC→TAC)	rpoB →	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,182,583	0	C	T	100.0%	190.3 / NA	51	H447Y (CAC→TAC)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (29/22); total (29/22)

TGCGGTTGGTCGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACCACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACG  >  NC_000913/4182438‑4182727

tGCGGTTGGTCGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAGGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTc                                                                                                                                             >  1:379255/1‑151 (MQ=255)

 gCGGTTGGTCGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCg                                                                                                                                            <  2:39229/151‑1 (MQ=255)

    gTTGGTCGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGc                                                                                                                                          >  2:467322/1‑150 (MQ=255)

       ggTCGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAAcc                                                                                                                                      <  1:177956/151‑1 (MQ=255)

          cGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACcgtc                                                                                                                                   >  2:400408/1‑151 (MQ=255)

            tATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACcgtcgt                                                                                                                                 >  1:421424/1‑151 (MQ=255)

             aTGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTa                                                                                                                                <  1:76436/151‑1 (MQ=255)

              tGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTAt                                                                                                                               >  1:205563/1‑151 (MQ=255)

                  gTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTAtccgt                                                                                                                           <  2:51787/151‑1 (MQ=255)

                    tCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTAtccgttc                                                                                                                         >  1:242466/1‑151 (MQ=255)

                     cAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTAtccgttc                                                                                                                         <  1:600612/150‑1 (MQ=255)

                        ccGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTAtccgttccggt                                                                                                                     <  2:8815/151‑3 (MQ=255)

                          gTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTgg                                                                                                                   >  1:291864/1‑151 (MQ=255)

                          gTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTgg                                                                                                                   <  1:458242/151‑1 (MQ=255)

                               ctgctgCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCg                                                                                                                 <  2:186786/148‑1 (MQ=255)

                                agctgcGCGAAGAAATCGAAGTATCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAATAAGCTCATCGATATCCGAAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGaaa                                                                                                              >  2:494636/2‑150 (MQ=255)

                                        gaagaaATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCggta                                                                                                      >  1:191319/1‑148 (MQ=255)

                                        gaagaaATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGaaa                                                                                                     <  1:502680/151‑1 (MQ=255)

                                         aagaaATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGaaaa                                                                                                    <  2:11657/151‑1 (MQ=255)

                                             aaTCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAg                                                                                                <  2:586017/151‑1 (MQ=255)

                                                  aaGGGTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTcc                                                                                            >  2:448256/1‑150 (MQ=255)

                                                     gTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGt                                                                                        >  1:500726/1‑151 (MQ=255)

                                                           gTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCt                                                                                  >  1:248352/1‑151 (MQ=255)

                                                             aTCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTgg                                                                                >  2:405992/1‑151 (MQ=255)

                                                               ccTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGAGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGt                                                                               >  2:62365/1‑150 (MQ=255)

                                                                      aaaGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCg                                                                                                         <  2:421435/117‑1 (MQ=255)

                                                                        aGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTag                                                                       >  1:571153/1‑149 (MQ=255)

                                                                           cgacATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGt                                                                  >  1:536214/1‑151 (MQ=255)

                                                                             acATCATTGATGTTATTAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGc                                                                <  1:79479/151‑1 (MQ=255)

                                                                              catcatTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCg                                                               >  2:486120/1‑151 (MQ=255)

                                                                                  atTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTg                                                            >  1:41123/1‑150 (MQ=255)

                                                                                      aTGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAaga                                                       <  1:142616/151‑1 (MQ=255)

                                                                                       tGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAag                                                        >  2:303078/1‑149 (MQ=255)

                                                                                        gTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGc                                                     <  1:88405/151‑1 (MQ=255)

                                                                                           aTGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCgtc                                                  >  2:639809/1‑151 (MQ=255)

                                                                                            tGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCAAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAACGAGCttc                                                  >  1:200245/1‑150 (MQ=255)

                                                                                                      cATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGc                                       <  1:24960/151‑1 (MQ=255)

                                                                                                       aTCGATATCCGTAACGGTAAAGGCGCAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGGACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTCGGCg                                      >  1:298864/1‑151 (MQ=255)

                                                                                                       aTCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGc                                       <  1:709153/150‑1 (MQ=255)

                                                                                                          gATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATc                                   <  2:482816/151‑1 (MQ=255)

                                                                                                           atatCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCt                                  >  1:682686/1‑151 (MQ=255)

                                                                                                             atCCGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTTGGCAACCGTCGTATCCGTTCTGTTGGCGATATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTATAGCGAGCGGTGAAAGAGCGTCTGTCACTGGGCGATCTgg                                >  2:448924/1‑151 (MQ=255)

                                                                                                               ccGTAACGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGAt                              >  1:486030/1‑151 (MQ=255)

                                                                                                                     cGGTAAAGGCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTg                        <  1:183788/151‑1 (MQ=255)

                                                                                                                             gCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCcaca                <  2:723207/151‑1 (MQ=255)

                                                                                                                             gCGAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCcac                 >  2:343451/1‑150 (MQ=255)

                                                                                                                               gAAGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAgg              >  2:310813/1‑151 (MQ=255)

                                                                                                                                aaGTCGATGATATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGa             <  2:103147/151‑1 (MQ=255)

                                                                                                                                       tgatATCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATc      >  1:245791/1‑151 (MQ=255)

                                                                                                                                           atCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACg  <  2:242442/151‑1 (MQ=255)

                                                                                                                                           atCGACTACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACg  >  2:316103/1‑151 (MQ=255)

TGCGGTTGGTCGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCCGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACCACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACG  >  NC_000913/4182438‑4182727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A