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 F112 I0 R1	62	38.0	1654010	89.9%	1486954	142.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,196,235	C→A	29.3%	intergenic (‑136/+97)	thiC ← / ← rsd	phosphomethylpyrimidine synthase/regulator of sigma D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,196,235	0	C	A	29.3%	73.7 / 28.6	54	intergenic (‑136/+97)	thiC/rsd	phosphomethylpyrimidine synthase/regulator of sigma D
Reads supporting (aligned to +/- strand): ref base C (17/21); new base A (10/6); total (27/27)
Fisher's exact test for biased strand distribution p-value = 3.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

CAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGAAT  >  NC_000913/4196093‑4196376

cAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATc                                                                                                                                               >  2:155543/1‑143 (MQ=255)

   aCATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGATGTGGGATGGGGCAAGAGACGATAGGCGAGGGTTCCACACCATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCg                                                                                                                                            >  1:604665/1‑143 (MQ=255)

    cATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATcccaa                                                                                                                                           >  1:297081/1‑141 (MQ=255)

     aTAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGaa                                                                                                                                          <  1:221655/143‑1 (MQ=255)

         cTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAACAATTTACTGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATaaa                                                                                                                                      <  1:599673/143‑1 (MQ=255)

            agtCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCTATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACgg                                                                                                                                   <  1:271012/141‑1 (MQ=255)

                cAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGCTGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATACCGAATAAACGGtctc                                                                                                                               >  1:33368/1‑143 (MQ=255)

                     aGTTGAGGACGTGGCGTGTCAGACGACGGAGGAAGCAAGAGGCGATCGCCGCAGGGGCGATGCGATAGCAGATTAGCTCTCGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATACCGAATAAACGGTCTCAGCCa                                                                                                                          <  2:785233/143‑1 (MQ=255)

                     aGTTACGTACGTGGCTTCTCAGACGACGGATGACGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTCACTATTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCa                                                                                                                          <  1:518637/143‑1 (MQ=255)

                     aGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAAGTTCCGCGGATCCCGAATAAACGGTCTCAGCCa                                                                                                                          >  2:686741/1‑143 (MQ=255)

                           ggACGTGGCTGGTGAGGCGACGGGTGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATGAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAg                                                                                                                    <  2:672080/143‑1 (MQ=255)

                              cGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCa                                                                                                                 <  2:566217/143‑1 (MQ=255)

                               gTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTAATAGCCTGATCAGGTTCCGCGGAACCCGAATAAACGGTCTCAGCCAGTTAAGGCAc                                                                                                                >  2:759236/1‑143 (MQ=255)

                                    ttGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGGTCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCgc                                                                                                           >  2:814836/1‑142 (MQ=255)

                                    atctCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGGATTAGCCTGATCAGGTTCCGCGGATACCGAATAAACGCTCTCACCCAGTTACGGCCCCCCGa                                                                                                           >  2:549713/4‑143 (MQ=255)

                                     tGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGAc                                                                                                          <  2:514483/143‑1 (MQ=255)

                                       tCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACaa                                                                                                        <  1:329035/143‑1 (MQ=255)

                                          gacgacGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGaa                                                                                                     >  1:331652/1‑143 (MQ=255)

                                           acgacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGaaa                                                                                                    >  1:683559/1‑143 (MQ=255)

                                                      aGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGCTACGGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCa                                                                                         >  2:713035/1‑143 (MQ=255)

                                                         aaGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAAt                                                                                      >  1:742508/1‑143 (MQ=255)

                                                            agaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAACTggg                                                                                   >  1:541601/1‑143 (MQ=255)

                                                              aCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGATCCGCGGATCGCGAATAAACGGTCTCATCCAGTTAAGGCACTACGACAAGACATTAGCCCCGCCAATGGGGc                                                                                 >  1:152854/1‑143 (MQ=255)

                                                                gATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGGATTAGCCTGATCAGGTTCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAAAGGGGCag                                                                               >  2:85936/1‑142 (MQ=255)

                                                                 aTCGCCGCATGGGCGATGCGATAGAAGAGGAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAtt                                                                              <  1:26584/143‑1 (MQ=255)

                                                                     ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                                                                          <  1:321118/143‑1 (MQ=255)

                                                                     ccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATACCGAATACACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                                                                          <  1:309261/143‑1 (MQ=255)

                                                                     ccgcAGGGGCGATGCGATAGCAGAGTAACTCTCGTTCCGTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                                                                          <  2:813498/143‑1 (MQ=255)

                                                                          ggggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCGCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTaaa                                                                     >  1:601692/1‑143 (MQ=255)

                                                                                         cAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATACGCGGTCCCCGCCAGTTCAGGCACTCCGACCAGAAATCAGCCCCGCCCGTGGGGCCGTCAACGTAACTCACGCGTACACAgc                                                      >  2:750928/1‑143 (MQ=255)

                                                                                          aGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAACTTAGCCCCGCCAATGGGGCGCTGAATGTAAATTACGCGGTCACcgcg                                                     >  1:322087/1‑143 (MQ=255)

                                                                                           gATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAgcgc                                                    >  1:426429/1‑143 (MQ=255)

                                                                                            aTTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCCTTGAATGTAAATTAAGCGTTAACCACGCa                                                   >  2:159327/1‑143 (MQ=255)

                                                                                            aTTAACTCGTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa                                                   <  1:683761/143‑1 (MQ=255)

                                                                                               aaCGCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGaa                                                <  1:2306/143‑1 (MQ=255)

                                                                                                       ttCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATCACGCGTTAACAGCGCAGAACTCGAGCa                                        >  2:249822/1‑143 (MQ=255)

                                                                                                       ttCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATACCGAATACACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCCTTGAATGTAAATTACGCGTTACCAGCGCAGAACTACAGCa                                        >  2:552804/1‑143 (MQ=255)

                                                                                                       ttCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCa                                        >  2:547090/1‑143 (MQ=255)

                                                                                                        tCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAg                                       <  1:218410/143‑1 (MQ=255)

                                                                                                          ccTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTACGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGa                                     >  2:97797/1‑143 (MQ=255)

                                                                                                           cTTCGCAGGTATTAGCCTGATCAGGTTCCGCGTATACCGAATCAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGAt                                    <  1:211199/143‑1 (MQ=255)

                                                                                                           cTTCGCAGGTATTAGCCTGATCAGGTGCCGCGGATCCCGAATGAACGGACACAGCCAGTTAAAGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCCTTGAATGTAAACTACGCGCTCACAGCGCAGAACTCAAGCacgct                                    >  2:572017/1‑139 (MQ=255)

                                                                                                            ttCGCAGGTATTAGCCTGCTCAGGTTCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATGAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATg                                   <  1:313224/143‑1 (MQ=255)

                                                                                                               gCAGGTATTAGCCTGATCAGGTTCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGttt                                <  2:742508/143‑1 (MQ=255)

                                                                                                                      ttAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACgcgg                         >  1:721180/1‑143 (MQ=255)

                                                                                                                      gtAGCCTGGTCAGGTCCCGCGGCTCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTAAAAGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACgcgg                         <  1:646722/142‑1 (MQ=255)

                                                                                                                          ccggATCAGGTCCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAGTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACgcgggcgg                     <  2:158912/140‑1 (MQ=255)

                                                                                                                            tGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGgcggcg                   <  2:426429/143‑1 (MQ=255)

                                                                                                                            tGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGgcggcg                   >  2:274269/1‑143 (MQ=255)

                                                                                                                                cAGGTTCCGTGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAACGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCaa               <  2:387246/143‑1 (MQ=255)

                                                                                                                                cAGGTTCCGCGGATCCCTAATAAACGGGCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCCGCCCGCGTCaa               <  2:79133/143‑1 (MQ=255)

                                                                                                                                 gggTTCCGCGGATCCCGAATAAACGGTGTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAg              <  2:448238/142‑1 (MQ=255)

                                                                                                                                   gTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCa            >  2:678106/1‑143 (MQ=255)

                                                                                                                                   gTTCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCa            >  2:629862/1‑143 (MQ=255)

                                                                                                                                    ttCCGCGGATACCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCAc           <  1:155543/143‑1 (MQ=255)

                                                                                                                                           gATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAAGGGGGCATTGAAGGTAAATGACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGa    <  1:669650/143‑1 (MQ=255)

                                                                                                                                             ccccGCATAAGCTGTCTCAGGCGGGTCAGGAAGCCCGACAAGAAATTGCCCCCGCAACTGGGGCATTGAATGTAAATTACGCGTTGACAGCGCAGAACGCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGAAt  <  2:456574/142‑1 (MQ=255)

CAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAGGATGTTTGACGCGGGCGGCGTCAAGCACCAGCAGAAT  >  NC_000913/4196093‑4196376

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A