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
A9 F22 I0 R1	151	71.0	1572916	92.9%	1461238	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,027,805	C→A	10.6%	V48F (GTT→TTT)	vraS ←	sensor histidine kinase VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,027,805	0	C	A	10.6%	207.9 / 10.8	63	V48F (GTT→TTT)	vraS	sensor histidine kinase VraS
Reads supporting (aligned to +/- strand): ref base C (25/31); new base A (3/4); total (28/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

ATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAGTGG  >  CP000730/2027665‑2027941

aTTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAc                                                                                                                                          <  1:55881/141‑1 (MQ=255)

 ttAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACACTAATATGATGATGAGATTTAAAAATAAAAAAACt                                                                                                                                         >  1:726377/1‑141 (MQ=255)

       ccAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTAtt                                                                                                                                   <  1:598330/141‑1 (MQ=255)

       ccAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTAtt                                                                                                                                   >  2:454317/1‑141 (MQ=255)

        cAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTc                                                                                                                                  <  1:139806/141‑1 (MQ=255)

          aCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCg                                                                                                                                <  1:248705/141‑1 (MQ=255)

           cTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGa                                                                                                                               >  1:602773/1‑141 (MQ=255)

             ttttCGCCTTACATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGAATAAAAAAAAAAAAAACTGGTATTCCGAat                                                                                                                             <  2:500262/140‑1 (MQ=255)

                   acTTCCATTGAACGCTCAATTTGCGTCTTAAACCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGAATAAAAAAAAAAAAAACTGGTATTCCGAATATTtgt                                                                                                                       <  2:312137/140‑1 (MQ=255)

                      tCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGta                                                                                                                    >  2:420302/1‑141 (MQ=255)

                       ccATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGtat                                                                                                                   >  1:617728/1‑141 (MQ=255)

                          ttGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATTAAAAAACTGGTATTCCGAATATTTGTGTATaaa                                                                                                                <  1:409446/141‑1 (MQ=255)

                          ttGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTAAGAATATTTGTGTATaaa                                                                                                                >  2:391997/1‑141 (MQ=255)

                              aCGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACAt                                                                                                            >  1:496239/1‑141 (MQ=255)

                                  tCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAAAGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCt                                                                                                        >  1:179919/1‑141 (MQ=255)

                                  tCAATTTGCGTCTTAATCCAATCATTTTGCCGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCt                                                                                                        >  2:394579/1‑141 (MQ=255)

                                           gTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAg                                                                                               >  1:453165/1‑141 (MQ=255)

                                           gTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAg                                                                                               >  2:297218/1‑141 (MQ=255)

                                            tCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAga                                                                                              <  1:528149/141‑1 (MQ=255)

                                               tAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAgatga                                                                                           <  1:548031/141‑1 (MQ=255)

                                                   ccAATCATTTTGCTGATTGGTTTTGTAAGTGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAtt                                                                                       <  2:754275/141‑1 (MQ=255)

                                                      atgaTTTTGCTGATTGATTTGGTAAGGGAGTACCGAACCAACATTAATACGGTATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTAc                                                                                    <  2:253985/138‑1 (MQ=255)

                                                      aTCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTAc                                                                                    <  1:139657/141‑1 (MQ=255)

                                                       tCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACa                                                                                   >  2:95695/1‑141 (MQ=255)

                                                       tCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACa                                                                                   <  1:420302/141‑1 (MQ=255)

                                                        cATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaa                                                                                  <  1:87310/141‑1 (MQ=255)

                                                           tttGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATCATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaaaa                                                                               >  1:769051/1‑141 (MQ=255)

                                                           tttGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAACACATACCTTTAAAATAGATGATATTTAcaacaa                                                                               >  1:303965/1‑141 (MQ=255)

                                                            ttGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAAc                                                                              <  1:53313/141‑1 (MQ=255)

                                                              gCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACtt                                                                            <  1:52827/141‑1 (MQ=255)

                                                                 gattgattTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTAt                                                                         <  1:190437/141‑1 (MQ=255)

                                                                                 gAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGc                                                         <  1:344591/141‑1 (MQ=255)

                                                                                  aGTACCGAACCAAAAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCa                                                        <  2:427979/141‑1 (MQ=255)

                                                                                   gTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAAccactacatta                                                       <  1:314468/141‑11 (MQ=255)

                                                                                    tACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGc                                                      <  1:681662/141‑1 (MQ=255)

                                                                                    tACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGACGAACAGAAATGCAGc                                                      >  2:27378/1‑141 (MQ=255)

                                                                                       cGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAg                                                   <  2:334261/141‑1 (MQ=255)

                                                                                               caaTAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAATAACTTTATCGATGAACAGAAATGCAGCTAGCATGCtat                                           <  1:416037/141‑1 (MQ=255)

                                                                                                  taataCACAACAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCtatata                                        >  1:192702/1‑141 (MQ=255)

                                                                                                   aataCACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATAc                                       <  2:286408/141‑1 (MQ=255)

                                                                                                   aataCACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCCTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAAAAATGCAGATGGCATGCtatattc                                       >  1:528934/1‑139 (MQ=255)

                                                                                                    ataCACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACt                                      <  1:300600/141‑1 (MQ=255)

                                                                                                     taCACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTa                                     >  2:337314/1‑141 (MQ=255)

                                                                                                         caATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGag                                 >  2:272644/1‑140 (MQ=255)

                                                                                                              atatGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTAGAAAAACTTTATCGATGAACAGAAATGCAGCTAGCAGGCTATATACTAAGATGAGCa                            >  1:783415/1‑141 (MQ=255)

                                                                                                                   atgatgaGATTTAAAAATAAAAAAACTGGTATTCCGAATCTTCGTGGATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGaa                       <  1:206706/141‑1 (MQ=255)

                                                                                                                   atgatgaGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGaa                       <  1:640720/141‑1 (MQ=255)

                                                                                                                     gatgaGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAAcc                     >  1:468714/1‑141 (MQ=255)

                                                                                                                       tgaGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCaa                   <  2:190097/141‑1 (MQ=255)

                                                                                                                         agaTTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAAtt                 <  1:583842/141‑1 (MQ=255)

                                                                                                                           aTTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGt               <  2:414234/141‑1 (MQ=255)

                                                                                                                            tttAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGtt              <  1:219698/141‑1 (MQ=255)

                                                                                                                            tttAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGtt              >  2:335392/1‑141 (MQ=255)

                                                                                                                              taaaaataaaaaAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCt            >  2:376394/1‑141 (MQ=255)

                                                                                                                              taaaaataaaaaAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCt            <  1:404436/141‑1 (MQ=255)

                                                                                                                                aaataaaaaaaaCTTGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTaa          >  2:359946/6‑141 (MQ=255)

                                                                                                                                aaaataaaaaAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTaa          >  2:563408/1‑141 (MQ=255)

                                                                                                                                aaaataaaaaAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTaa          >  1:579663/1‑141 (MQ=255)

                                                                                                                                    taaaaaAACTGGTATTCCGATTATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTa      <  2:726377/141‑1 (MQ=255)

                                                                                                                                    taaaaaAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTa      <  1:63556/141‑1 (MQ=255)

                                                                                                                                    aaaaaaaaCTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTa      <  2:181139/140‑1 (MQ=255)

                                                                                                                                     aaaaaaaCTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAg     <  2:603239/141‑1 (MQ=255)

                                                                                                                                      aaaaaaCTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAGt    >  1:475164/1‑141 (MQ=255)

                                                                                                                                        aaaaCTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAGTgg  >  1:448819/1‑141 (MQ=255)

ATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAGTGG  >  CP000730/2027665‑2027941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `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