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
A15 F70 I1 R1	16	113.5	2638332	93.5%	2466840	136.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,522,286	A→G	P782P (CCT→CCC)	nasD ←	Nitrite reductase [NAD(P)H]

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,522,286	0	A	G	97.6%	423.0 / ‑2.1	127	P782P (CCT→CCC)	nasD	Nitrite reductase [NAD(P)H]
Reads supporting (aligned to +/- strand): ref base A (2/1); new base G (58/63); total (62/65)
Fisher's exact test for biased strand distribution p-value = 6.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 127 total aligned reads displayed.

AATAACCTTTTTTCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAAGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTCAGCAT  >  USA300TCH1516_ALE/2522151‑2522419

aaTAACCTTTTTTCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTc                                                                                                                                  <  1:216679/141‑1 (MQ=255)

   aaCCTTTTTTCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGc                                                                                                                               >  3:309909/1‑141 (MQ=255)

   aaCCTTTTTTCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGc                                                                                                                               >  1:359646/1‑141 (MQ=255)

        tttttCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGa                                                                                                                          <  2:45984/141‑1 (MQ=255)

         ttttCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGAc                                                                                                                         >  1:918752/1‑141 (MQ=255)

         ttttCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGAc                                                                                                                         >  3:268614/1‑141 (MQ=255)

          tttCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACt                                                                                                                        >  2:282489/1‑141 (MQ=255)

            tCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGc                                                                                                                      <  2:824675/141‑1 (MQ=255)

               aaTTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTTTTTTTTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCttt                                                                                                                   >  2:739339/1‑141 (MQ=255)

                 ttAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCttttt                                                                                                                 <  1:618302/141‑1 (MQ=255)

                     gggTGTTAATTCATCTATAGTTGTCACTTTAAGTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGc                                                                                                             <  2:673469/141‑1 (MQ=255)

                      ggTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCa                                                                                                            >  2:746924/1‑141 (MQ=255)

                         gtTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATcc                                                                                                         <  1:466237/141‑1 (MQ=255)

                           tAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCAt                                                                                                       <  4:100260/141‑1 (MQ=255)

                             aTTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATaa                                                                                                     >  1:819146/1‑141 (MQ=255)

                               tCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGAGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATg                                                                                                   >  3:288168/1‑141 (MQ=255)

                                cATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCTAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGc                                                                                                  <  2:892853/141‑1 (MQ=255)

                                cATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGc                                                                                                  <  2:395018/141‑1 (MQ=255)

                                  tCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATTCGt                                                                                                >  2:858536/1‑141 (MQ=255)

                                     ataGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCa                                                                                             >  1:121937/1‑141 (MQ=255)

                                      taGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCaa                                                                                            >  3:364741/1‑141 (MQ=255)

                                       aGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCaaa                                                                                           <  1:282489/141‑1 (MQ=255)

                                        gTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAAt                                                                                          <  2:371439/141‑1 (MQ=255)

                                          tGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAg                                                                                        >  2:914919/1‑141 (MQ=255)

                                            tCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCCGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAAtcctt                                                                                      >  2:666972/1‑137 (MQ=255)

                                             cACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTc                                                                                     <  4:111854/141‑1 (MQ=255)

                                             cACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTc                                                                                     >  1:127915/1‑141 (MQ=255)

                                             cACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTc                                                                                     <  1:492406/141‑1 (MQ=255)

                                              aCTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAAt                                                                                                    >  1:31978/1‑125 (MQ=255)

                                              aCTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAAt                                                                                                    <  2:31978/125‑1 (MQ=255)

                                              aCTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCa                                                                                    >  1:579348/1‑141 (MQ=255)

                                              aCTTTAATTTTTTCTTTTGTTTACATGTATTACACCTTCTGCAATTCAAAAATTCTACGTGGTTGCGTATTGCTAGTTATTGCTGCCAAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGTGTTCAAATAGTTCa                                                                                    >  2:546270/1‑141 (MQ=255)

                                               cTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCAt                                                                                   <  1:344251/141‑1 (MQ=255)

                                                 ttAATTTTCTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCAttt                                                                                 <  4:319171/141‑1 (MQ=255)

                                                   aaTTTTTTTTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCATGGTTCAGCTTCGACTGCTTTTTTAGCACCCAGAATGCGTTCAAATAGTTCATTTTg                                                                               <  4:357731/141‑1 (MQ=255)

                                                   aaTTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTg                                                                               <  4:271050/141‑1 (MQ=255)

                                                   aaTTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTg                                                                               <  2:257633/141‑1 (MQ=255)

                                                      tttttCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCt                                                                            <  1:127430/141‑1 (MQ=255)

                                                      tttttCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCt                                                                            <  1:429989/141‑1 (MQ=255)

                                                         ttCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTc                                                                         >  3:369747/1‑141 (MQ=255)

                                                          tCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCt                                                                        >  1:874220/1‑141 (MQ=255)

                                                            ttttGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTgg                                                                      <  2:428438/141‑1 (MQ=255)

                                                            ttttGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTgg                                                                      <  4:282413/141‑1 (MQ=255)

                                                               ttttttCATGTATTACACCTTCTCCACTTCAAAAATTTTACGTGCTTGCGCATTGCTAGTTATTGCTTCCTTTTTTTCTTTTTTGTCTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCTTTTTGTCTTTCTGGTTc                                                                   >  2:763802/3‑141 (MQ=255)

                                                                     cATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTaa                                                             <  2:440673/141‑1 (MQ=255)

                                                                      aTGTATTACCCCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTGGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAg                                                            <  1:362486/141‑1 (MQ=255)

                                                                      aTGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCtttt                                                                                                                  >  2:140697/1‑87 (MQ=255)

                                                                      aTGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCtttt                                                                                                                  <  1:140697/87‑1 (MQ=255)

                                                                      aTGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAg                                                            >  3:50626/1‑141 (MQ=255)

                                                                       tGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGa                                                           <  1:699810/141‑1 (MQ=255)

                                                                         tATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGAct                                                         >  1:483813/1‑141 (MQ=255)

                                                                           ttACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGActtc                                                       <  1:223852/141‑1 (MQ=255)

                                                                           ttACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGActtc                                                       >  2:592445/1‑141 (MQ=255)

                                                                            tACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGActtct                                                      >  1:537760/1‑141 (MQ=255)

                                                                             acacCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCaa                                                                                            <  2:713582/102‑1 (MQ=255)

                                                                             acacCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCaa                                                                                            >  1:713582/1‑102 (MQ=255)

                                                                             acacCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGActtctt                                                     >  1:404321/1‑141 (MQ=255)

                                                                              cacCTTCTCCGCTTCATAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCGATGATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCttt                                                    <  2:774700/141‑1 (MQ=255)

                                                                              cacCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCttt                                                    <  4:268614/141‑1 (MQ=255)

                                                                              cacCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCttt                                                    <  2:628235/141‑1 (MQ=255)

                                                                                   tctcCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACAt                                               <  3:397383/141‑1 (MQ=255)

                                                                                    ctcCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACAtt                                              >  1:815848/1‑141 (MQ=255)

                                                                                    ctcCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACAtt                                              <  2:64604/141‑1 (MQ=255)

                                                                                    ctcCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACAtt                                              <  1:688088/141‑1 (MQ=255)

                                                                                      ccACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACAtttt                                            <  1:860963/141‑1 (MQ=255)

                                                                                      ccACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACAtttt                                            <  2:510119/141‑1 (MQ=255)

                                                                                      ccACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACAtttt                                            <  1:579480/141‑1 (MQ=255)

                                                                                       cACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTc                                           <  1:398141/141‑1 (MQ=255)

                                                                                          ttCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTgg                                                                      <  1:652402/111‑1 (MQ=255)

                                                                                            cAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATc                                      <  4:267836/141‑1 (MQ=255)

                                                                                            aaataaTTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAAGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGCGTCAAGTAAGACTTCTTTTACATTTTCAAATc                                      <  2:137328/137‑1 (MQ=255)

                                                                                             aaaaaTTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATcc                                     <  2:297148/141‑1 (MQ=255)

                                                                                                aaTTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAg                                  >  1:218563/1‑141 (MQ=255)

                                                                                                  ttCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGtc                                <  4:151610/141‑1 (MQ=255)

                                                                                                   tCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCTACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGtct                               >  2:4663/1‑141 (MQ=255)

                                                                                                     tACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGtcttc                             <  2:359646/141‑1 (MQ=255)

                                                                                                        gTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTa                          >  1:635596/1‑141 (MQ=255)

                                                                                                        gTGCTTGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTa                          >  3:245892/1‑141 (MQ=255)

                                                                                                            ttGCGCATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCa                      <  2:397386/141‑1 (MQ=255)

                                                                                                              gcgcATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATg                    >  2:597958/1‑141 (MQ=255)

                                                                                                              gagcATTGCTAGTTATTGCTTCCCAGGATTCAGCTTCGACTGCTTATTTATCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTATGACTTCTTTTAAATTTTCAAATCCAACTATTCTTAACCATg                    >  2:270308/3‑141 (MQ=255)

                                                                                                                 cATTGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGgcg                 >  2:349989/1‑141 (MQ=255)

                                                                                                                 cATGGCTAGATATTGCTTCAAAGGGTTCAGCTATTACTTCTTTTTTAGCAGCCGCAAACCGTTCAAATAGTTCGTTTTGTCTTTCTGGGGCAAGTAAGACTTCCTCTACATTTTCAAATCCAAGTCTTGTTAACCaatgcg                 >  2:732496/1‑136 (MQ=255)

                                                                                                                   ttGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCt               <  4:349594/141‑1 (MQ=255)

                                                                                                                    tGCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTGAAATGGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATGTTCAAATCCAAGTCTTCTTAACCATGGCGCTg              <  2:572285/141‑1 (MQ=255)

                                                                                                                     gCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGgc                  <  2:239947/136‑1 (MQ=255)

                                                                                                                     gCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGgc                  >  1:239947/1‑136 (MQ=255)

                                                                                                                     gCTAGTTATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGt             >  1:325409/1‑141 (MQ=255)

                                                                                                                         gTTATTGCTTCCCAAGGATCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGCCTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCtt         >  2:395492/1‑141 (MQ=255)

                                                                                                                           tATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTc       >  3:180541/1‑141 (MQ=255)

                                                                                                                           tATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTc       >  3:180536/1‑141 (MQ=255)

                                                                                                                           tATTGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTc       >  2:255488/1‑141 (MQ=255)

                                                                                                                             ttGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTCAg     <  3:187019/141‑1 (MQ=255)

                                                                                                                             ttGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTCAg     <  1:438567/141‑1 (MQ=255)

                                                                                                                             ttGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTCAg     <  1:49634/141‑1 (MQ=255)

                                                                                                                             ttGCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTCAg     <  1:739339/141‑1 (MQ=255)

                                                                                                                               gCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCt                                                                        >  2:281537/1‑72 (MQ=255)

                                                                                                                               gCTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCt                                                                        <  1:281537/72‑1 (MQ=255)

                                                                                                                                cTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTCAGCat  >  1:635225/1‑141 (MQ=255)

                                                                                                                                cTTCCCAGGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTCAGCat  >  2:583547/1‑141 (MQ=255)

AATAACCTTTTTTCCAATTAGGGGTGTTAATTCATCTATAGTTGTCACTTTAATTTTTTCTTTTGTTTCCATGTATTACACCTTCTCCACTTCAAAAATTCTACGTGCTTGCGCATTGCTAGTTATTGCTTCCCAAGGTTCAGCTTCGACTGCTTTTTTAGCATCCATAATGCGTTCAAATAGTTCATTTTGTCTTTCTGGGTCAAGTAAGACTTCTTTTACATTTTCAAATCCAAGTCTTCTTAACCATGGCGCTGTTCTTTCAGCAT  >  USA300TCH1516_ALE/2522151‑2522419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A