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
A7 F50 I2 R1	209	44.2	1360995	98.7%	1343302	150.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,779,043	A→G	M549V (ATG→GTG)	lldP →	L‑lactate permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,779,043	0	A	G	97.9%	176.6 / ‑2.8	48	M549V (ATG→GTG)	lldP	L‑lactate permease
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (26/21); minor base C (1/0); total (27/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

CCCCGCAATCTATCGCTATCGCCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGATGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCGGCGTATCACGT  >  NC_000913/3778897‑3779188

ccccGCAATCTATCGCTATCGCCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGggtg                                                                                                                                                 <  1:379718/149‑1 (MQ=255)

      aaTCTATCGCTATCGCCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCtt                                                                                                                                          <  2:593861/150‑1 (MQ=255)

       aTCTATCGCTATCGCCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTa                                                                                                                                         >  1:182398/1‑150 (MQ=255)

        tCTATCGCTATCGCCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAAt                                                                                                                                       >  1:317221/1‑151 (MQ=255)

          tatcgctatcgcCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATg                                                                                                                                      >  1:578893/1‑150 (MQ=255)

               ctatcgcCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGCTGATTCCTTAATGATTGtt                                                                                                                                >  2:107859/1‑151 (MQ=255)

                    gcCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTAcc                                                                                                                           <  1:255223/151‑1 (MQ=255)

                       tgtgCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTAccc                                                                                                                          >  2:20417/1‑149 (MQ=255)

                        gtgCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCTCGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCa                                                                                                                         <  2:85024/149‑1 (MQ=255)

                          gcggcgGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGAc                                                                                                                      <  1:233510/150‑1 (MQ=255)

                          gcggcgGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGAc                                                                                                                      <  2:426929/150‑1 (MQ=255)

                           cggcggTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGc                                                                                                                    >  2:202942/1‑151 (MQ=255)

                                        ggtggGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGAGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAgg                                                                                                       >  1:665738/1‑151 (MQ=255)

                                         gtggGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGt                                                                                                      <  2:511760/151‑1 (MQ=255)

                                                 agagTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATc                                                                                              <  2:608358/151‑1 (MQ=255)

                                                  gagTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCg                                                                                             <  2:189916/151‑1 (MQ=255)

                                                  gagTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCg                                                                                             <  1:489743/151‑1 (MQ=255)

                                                   agTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCgt                                                                                            >  2:509526/1‑151 (MQ=255)

                                                        gANTTGTNCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGc                                                                                        <  2:70024/150‑1 (MQ=255)

                                                              ttCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCt                                                                                 >  1:497287/1‑151 (MQ=255)

                                                                     ttACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCtgattga                                                                           <  1:404413/150‑1 (MQ=255)

                                                                             aaaCACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGaaaaaa                                                                   >  1:49947/1‑150 (MQ=255)

                                                                                cacaGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAAcc                                                                >  2:435466/1‑150 (MQ=255)

                                                                                  caGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTgg                                                             <  1:232489/151‑1 (MQ=255)

                                                                                    gCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGaa                                                           <  1:369182/151‑1 (MQ=255)

                                                                                     ccTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAg                                                          <  2:196712/151‑1 (MQ=255)

                                                                                         aTCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCggg                                                      >  2:536612/1‑151 (MQ=255)

                                                                                          tCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGc                                                     >  1:253388/1‑151 (MQ=255)

                                                                                             tCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATg                                                  >  2:293263/1‑151 (MQ=255)

                                                                                               aCCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGaa                                                <  1:446468/151‑1 (MQ=255)

                                                                                                ccTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGa                                                 >  2:325582/1‑149 (MQ=255)

                                                                                                   gTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTg                                            <  1:445998/151‑1 (MQ=255)

                                                                                                      taGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGccc                                         >  1:16808/1‑151 (MQ=255)

                                                                                                      taGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGccc                                         >  1:626314/1‑151 (MQ=255)

                                                                                                         tGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCt                                      >  2:589450/1‑151 (MQ=255)

                                                                                                         tGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCt                                      >  2:605453/1‑151 (MQ=255)

                                                                                                         tGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCt                                      >  1:322356/1‑151 (MQ=255)

                                                                                                          gggCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTg                                     >  2:224332/1‑151 (MQ=255)

                                                                                                           ggCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTg                                     >  2:122417/1‑150 (MQ=255)

                                                                                                              gTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAgcg                                 <  1:587759/151‑1 (MQ=255)

                                                                                                                gATCACCACGCTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGcc                               >  2:642356/1‑151 (MQ=255)

                                                                                                                          cTTCAGGCTTATGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGAt                     >  1:509030/1‑151 (MQ=255)

                                                                                                                                    aTGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCgg            <  2:236537/150‑1 (MQ=255)

                                                                                                                                    aTGTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCGGc           <  2:567552/151‑1 (MQ=255)

                                                                                                                                      gTCTTAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCGGCGt         <  2:545205/151‑1 (MQ=255)

                                                                                                                                          tAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCGGCGTATc      >  2:404508/1‑150 (MQ=255)

                                                                                                                                          tAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCGGCGTATc      >  2:521624/1‑150 (MQ=255)

                                                                                                                                          tAACGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCGGCGTATc      >  1:149727/1‑150 (MQ=255)

                                                                                                                                             cGTGGGTGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCGGCGTATCACGt  <  1:448548/151‑1 (MQ=255)

CCCCGCAATCTATCGCTATCGCCTGTGCGGCGGTAGGCCTGGTGGGCAAAGAGTCTGATTTGTTCCGCTTTACTGTCAAACACAGCCTGATCTTCACCTGTATAGTGGGCGTGATCACCACGCTTCAGGCTTATGTCTTAACGTGGATGATTCCTTAATGATTGTTTTACCCAGACGCCTGTCAGACGAGGTTGCCGATCGTGTGCGGGCGCTGATTGATGAAAAAAACCTGGAAGCGGGCATGAAGTTGCCCGCTGAGCGCCAACTGGCGATGCAACTCGGCGTATCACGT  >  NC_000913/3778897‑3779188

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A