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 F17 I0 R1	71	50.6	2132758	90.5%	1930145	142.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,184,543	C→A	100%	P1100Q (CCG→CAG)	rpoB →	RNA polymerase subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,543	0	C	A	100.0%	171.6 / NA	54	P1100Q (CCG→CAG)	rpoB	RNA polymerase subunit beta
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (30/24); total (30/24)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCC  >  NC_000913/4184407‑4184680

gCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTggg                                                                                                                                     >  1:593795/1‑143 (MQ=255)

 cGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGc                                                                                                                                    <  1:421647/143‑1 (MQ=255)

  ggTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGGACTGAACCAGCTGGGCg                                                                                                                                   >  1:395490/1‑143 (MQ=255)

         cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCCCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCggc                                                                                                                            >  2:540624/1‑141 (MQ=255)

           cggTATCCAGCCTGGTGATAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                          <  1:294033/141‑1 (MQ=255)

           ccataaccAGCCTGGTGACAAGATGGCAGGACGGCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                          <  1:276574/137‑1 (MQ=255)

            cGTATCCGGCCGGGTGACAAGATGGCAGGTCGGCACGGTAACAAGGGTGTAATGTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTCCCGTCTCg                                                                                                                         <  2:275763/143‑1 (MQ=255)

              tATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGCCGTACCGGCTCGTa                                                                                                                       >  2:1004192/1‑143 (MQ=255)

              tATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGCAACGACCACAGTCGGCGTACTGAACCAGCTGGGCGTACCGTCTCGTa                                                                                                                       >  2:747915/1‑143 (MQ=255)

               aTCCAGCCTGGTGGCAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                      <  2:303888/143‑1 (MQ=255)

                 ccAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGa                                                                                                                    <  1:780882/143‑1 (MQ=255)

                        cgTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCAGATCGAAGATATGCCTTACGATGTAAACGGTACGCCGGTAGACATCGAACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCgg                                                                                                             >  2:1014873/2‑143 (MQ=255)

                         gTGACAAGAGGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAAACCGGTCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGt                                                                                                            <  1:489617/143‑1 (MQ=255)

                          tGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTc                                                                                                           <  1:383609/143‑1 (MQ=255)

                             cAAGATGGCAAGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGa                                                                                                        <  2:491452/143‑1 (MQ=255)

                                  tGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                   <  2:954666/143‑1 (MQ=255)

                                   ggCACGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCg                                                                                                  <  2:47521/143‑1 (MQ=255)

                                        gtcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTAAGCCGGGAGACATCGTACTGAACCAACTGGGCGTACCGACTCGTATGAACATCGGTCAGACCCTCGaagcg                                                                                             >  2:782518/1‑140 (MQ=255)

                                           gtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTCTGAACATCGGTCCGATCCTCGAAACCCAc                                                                                          >  1:28638/1‑143 (MQ=255)

                                            tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAcc                                                                                         >  1:973229/1‑143 (MQ=255)

                                               cGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                      >  1:594531/1‑143 (MQ=255)

                                                      aaGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTCAACCAACTAGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCCCGTGGAGATGGc                                                                               >  2:863420/1‑143 (MQ=255)

                                                        cggTGTAATTGCGAAGATCAACGCGCTCGAATAGATGCCGTACGATGAAAACGGGACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAACGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTg                                                                             <  1:114292/142‑1 (MQ=255)

                                                          gtgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCg                                                                           >  1:742973/1‑143 (MQ=255)

                                                              aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGACCATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                       <  2:851121/143‑1 (MQ=255)

                                                                  tCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGCACTGACCCAGCTGGGCGTACCGTCTCGTATGCGCATCGGTCAGATCCTCGGAACCCACCTGGGGATGCCTGCGCAAGGTAt                                                                   >  2:36776/1‑143 (MQ=255)

                                                                   cTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATc                                                                  >  2:201277/1‑143 (MQ=255)

                                                                    tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                                 >  1:369540/1‑143 (MQ=255)

                                                                        aTCAGCCCGATCGAAGATATGCCTTGCGAGGGAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                             <  2:647245/143‑1 (MQ=255)

                                                                        aTCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTACCGGCGa                                                             >  2:860538/1‑143 (MQ=255)

                                                                        aTCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGTGTGGCTGCGAAAGGTATCGGCGa                                                             >  1:128642/1‑143 (MQ=255)

                                                                         tCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGAc                                                            >  1:1031646/1‑143 (MQ=255)

                                                                         tCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGAc                                                            >  1:526145/1‑143 (MQ=255)

                                                                           aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                          >  1:911549/1‑143 (MQ=255)

                                                                            aCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGGCTCGTATGAGCCTCGGTCAGATCCTCGAAACCCCCCGCAGTATGCCTGCGAACGGCATGGCGGACaac                                                         >  1:850578/1‑142 (MQ=255)

                                                                             cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                        <  1:274517/143‑1 (MQ=255)

                                                                                  tCGAAGATATGCCTTACGCTGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                                   <  1:985849/143‑1 (MQ=255)

                                                                                    gAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGATACCCCCCTGGGTTTGGCTGCGAAAGGTATCGGAGACAAGATCAACGc                                                 >  1:7758/1‑143 (MQ=255)

                                                                                       gATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGCAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCAt                                              >  1:106414/1‑143 (MQ=255)

                                                                                        atatGCCTGACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGCCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATg                                             <  1:434890/143‑1 (MQ=255)

                                                                                               ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGATCAGATCCTCGAAACCCACCCGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAc                                      >  2:154218/1‑143 (MQ=255)

                                                                                                   gATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGCAACCCACCTGGGTATGGCTGCGAAAGGCATCGGCGACAAGATCAACCGCATCCTGAAAcagca                                  >  2:512805/1‑143 (MQ=255)

                                                                                                   catcaaaaCGTTACGCCTGTAGACATCGTACTCAACCAGCTGGGCGTACCGTCTCGTATGAACATCAACCAAAACGACTTGGTGCTCCTGGGTATGGCTGCGAAATGTATCGGCGACAAGATCAACGCCATGCTGAAAcagca                                  <  1:149295/139‑1 (MQ=255)

                                                                                                       aaaaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaa                              <  1:201277/143‑1 (MQ=255)

                                                                                                             gTACGCCGGTAGACATCGTACTGACCCAGCCGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTc                        <  1:1000875/143‑1 (MQ=255)

                                                                                                              tACGCTGGTAGACATCGTACTGAACCAGCTGGGAGTACCGGCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                       <  1:833505/143‑1 (MQ=255)

                                                                                                                         aCATCGTACCGAACAAGCTGGGCTTACCGGCTCGTATGAACATCGGTCAGATGCGCGAAACCCACCTGGGTATGGCTGCGAAAGGTAGCGGCGACACGACCAAAGCATTGCTGAAGCAGCAGCAAGAAGTCGCGAAACTgcgc            <  2:475153/143‑1 (MQ=255)

                                                                                                                           aTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGa          <  1:750601/143‑1 (MQ=255)

                                                                                                                            tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa         >  1:897281/1‑143 (MQ=255)

                                                                                                                            tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATAGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGGAGCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTTGCGAAACTGCGCGaa         >  1:266213/1‑143 (MQ=255)

                                                                                                                             cGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAGCAACGCCATGCTGAAACCGCACCAAGAAGCCGCGAAACTGCGCGAAt        >  2:294405/1‑143 (MQ=255)

                                                                                                                              gTACTGAGCCAGGTGGGCGTACCGTCGCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAtt       <  1:751200/143‑1 (MQ=255)

                                                                                                                                  tGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAGCTGCGCGAATTCATc   >  2:273963/1‑143 (MQ=255)

                                                                                                                                   gAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGAGAAGGTCAACGCCATGCTGAAACAGCAGCAAGAAGGCGCCAACGCGCGCGAATGAATcc  >  2:462248/1‑143 (MQ=255)

GCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCC  >  NC_000913/4184407‑4184680

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