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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,474,138	(A)_6→7	coding (15/594 nt)	bdcR →	transcriptional repressor for divergent bdcA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,474,132	1	.	A	96.8%	197.2 / ‑1.3	63	coding (9/594 nt)	bdcR	transcriptional repressor for divergent bdcA
Reads supporting (aligned to +/- strand): ref base . (0/2); new base A (35/26); total (35/28)
Fisher's exact test for biased strand distribution p-value = 1.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTTGG  >  NC_000913/4474013‑4474263

ccACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTAATATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGtt                                                                                                                   >  1:163934/1‑139 (MQ=255)

  aCCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTcc                                                                                                                 >  2:288548/1‑139 (MQ=255)

                   tCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGtt                                                                                                >  2:697300/1‑139 (MQ=255)

                   tCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGtt                                                                                                >  1:415833/1‑139 (MQ=255)

                             aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAAtctc                                                                                                                        <  2:636216/105‑1 (MQ=255)

                             aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAAtctc                                                                                                                        >  1:636216/1‑105 (MQ=255)

                               aaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGc                                                                                    >  2:477156/1‑139 (MQ=255)

                                  cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                               <  2:430899/125‑1 (MQ=255)

                                  cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                               >  1:430899/1‑125 (MQ=255)

                                               tCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                               >  2:541784/1‑112 (MQ=255)

                                               tCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                               <  1:541784/112‑1 (MQ=255)

                                               tCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGc                                                                    >  1:118005/1‑139 (MQ=255)

                                                 cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                  >  2:235626/1‑139 (MQ=255)

                                                           tatGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTc                                                                                          >  2:194226/1‑105 (MQ=255)

                                                           tatGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTc                                                                                          <  1:194226/105‑1 (MQ=255)

                                                               tAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                               >  1:317829/1‑96 (MQ=255)

                                                               tAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                               <  2:317829/96‑1 (MQ=255)

                                                               tAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                     <  1:704791/106‑1 (MQ=255)

                                                               tAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                     >  2:704791/1‑106 (MQ=255)

                                                                 aCATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCa                                                  >  1:421706/1‑139 (MQ=255)

                                                                  cATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGa                                                                                                    <  2:898481/88‑1 (MQ=255)

                                                                  cATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGa                                                                                                    >  1:898481/1‑88 (MQ=255)

                                                                  cATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaa                                                 >  1:222972/1‑139 (MQ=255)

                                                                  cATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaa                                                 >  2:19721/1‑139 (MQ=255)

                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAAtctc                                                                                                                        >  2:820201/1‑66 (MQ=255)

                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAAtctc                                                                                                                        <  1:820201/66‑1 (MQ=255)

                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTcg                                                                                                                       <  2:898152/67‑1 (MQ=255)

                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTcg                                                                                                                       >  1:898152/1‑67 (MQ=255)

                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                               <  1:19721/139‑1 (MQ=255)

                                                                     gCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAAtctc                                                                                                                        <  1:279837/65‑1 (MQ=255)

                                                                     gCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAAtctc                                                                                                                        >  2:279837/1‑65 (MQ=255)

                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAgg                                                                                                              <  2:738117/73‑1 (MQ=255)

                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAgg                                                                                                              >  1:738117/1‑73 (MQ=255)

                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAgg                                            >  1:129959/1‑139 (MQ=255)

                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAgg                                            >  2:740601/1‑139 (MQ=255)

                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAgg                                            >  2:753314/1‑139 (MQ=255)

                                                                         tACAAAACTGTTTTAACTCTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAgg                                                                                                              >  2:421545/1‑71 (MQ=255)

                                                                         tACAAAACTGTTTTAACTCTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAgg                                                                                                              <  1:421545/71‑1 (MQ=255)

                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt                                     <  1:477156/139‑1 (MQ=255)

                                                                                cTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGc                                   >  1:338992/1‑139 (MQ=255)

                                                                                   ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt                                     >  1:759312/1‑134 (MQ=255)

                                                                                   ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt                                     <  2:759312/134‑1 (MQ=255)

                                                                                   ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                                <  2:222972/139‑1 (MQ=255)

                                                                                      tAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                             <  1:288548/139‑1 (MQ=255)

                                                                                      tAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                             <  2:384773/139‑1 (MQ=255)

                                                                                           ttCTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTg                        >  2:919088/1‑139 (MQ=255)

                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                             >  2:121331/1‑132 (MQ=255)

                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                             <  1:121331/132‑1 (MQ=255)

                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCt                      <  2:338992/139‑1 (MQ=255)

                                                                                              tGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                  >  2:366834/1‑94 (MQ=255)

                                                                                              tGTCAACAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                  <  1:366834/94‑1 (MQ=255)

                                                                                                  aaCAGGTTTTGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt                 <  2:242171/139‑1 (MQ=255)

                                                                                                  aaCAGGTTTTGTAATGGTCACT‑AA‑AAACACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt                 <  2:118005/139‑1 (MQ=255)

                                                                                                   aCAGGTTTTGTAATGGTCACT‑AAGAAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGtt                <  2:163934/139‑1 (MQ=255)

                                                                                                          ttGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGAtt         >  1:441517/1‑139 (MQ=255)

                                                                                                          ttGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGAt          <  2:27467/138‑1 (MQ=255)

                                                                                                          ttGTAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGAt          >  1:27467/1‑138 (MQ=255)

                                                                                                             tAATGGTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATc      <  2:441517/139‑1 (MQ=255)

                                                                                                                 ggTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCttttt                                                       >  2:344590/1‑86 (MQ=255)

                                                                                                                 ggTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCttttt                                                       <  1:344590/86‑1 (MQ=255)

                                                                                                                 ggTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt                 >  2:714688/1‑124 (MQ=255)

                                                                                                                 ggTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt                 <  1:714688/124‑1 (MQ=255)

                                                                                                                 ggTCACTAAA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTTgg  >  1:673535/1‑139 (MQ=255)

CCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AA‑AAA‑ACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTTGG  >  NC_000913/4474013‑4474263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A