BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,440,007	Δ1 bp	coding (34/201 nt)	cspA_2 ←	Cold shock protein CspA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,440,007	0	C	.	98.3%	547.5 / 1.4	118	coding (34/201 nt)	cspA_2	Cold shock protein CspA
Reads supporting (aligned to +/- strand): ref base C (0/0); major base . (48/68); minor base T (0/2); total (48/70)
Fisher's exact test for biased strand distribution p-value = 5.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

Only 100 of 118 total aligned reads displayed.

CTTGTGGACCGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCT  >  USA300TCH1516_ALE/1439863‑1440151

   gtgGACCGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATGCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTaa                                                                                                                                          <  2:364971/149‑1 (MQ=255)

   gtgGACCGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTaa                                                                                                                                          <  1:651615/149‑1 (MQ=255)

   gtgGACCGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTaa                                                                                                                                          <  1:1381148/149‑1 (MQ=255)

     ggACCGCGGTTGCCTTCAACTACTTCAACCTCAACAGCTTGACCTTCTTCTAATGATTTGTACCCGTCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAAc                                                                                                                                        <  1:826087/149‑1 (MQ=255)

     ggACCGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAAc                                                                                                                                        <  1:1665715/149‑1 (MQ=255)

     ggACCGCGGGCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAAc                                                                                                                                        <  1:518556/149‑1 (MQ=255)

     ggACCGCGGCCGCCTTCAACTACTCCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAAc                                                                                                                                        <  1:782099/149‑1 (MQ=255)

            ggTCGCCTTCAACTGCTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTaa                                                                                                                                 <  1:959594/149‑1 (MQ=255)

               cGCCTTCAACTACTTCCACCTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTg                                                                                                                              <  2:1335946/149‑1 (MQ=255)

                 ccTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATCATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTa                                                                                                                            <  2:1433852/149‑1 (MQ=255)

                 ccTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCGAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTa                                                                                                                            <  1:1423515/149‑1 (MQ=255)

                   ttCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTAcc                                                                                                                          >  2:78336/1‑149 (MQ=255)

                      aaCTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTAGCTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTg                                                                                                                       >  2:1046334/1‑149 (MQ=255)

                       actactTCAAACTCAACAGCTTGAGATTGTTTTTATGTTTTGGAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCATTCAACTTCGATAAAGGCGAATCCTTTTT‑AGCGTTAAACCATTTAACTATACCTTGt                                                                                                                      >  2:371610/1‑149 (MQ=255)

                       actactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATCGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGt                                                                                                                      >  2:783194/1‑149 (MQ=255)

                         tactTCAGTCGCAACAGCGTGACCTTCTTCCAATGATTTGTAACCCTCTTGGTTAATTGCTGAAAAATGTACTAATACGGCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGttt                                                                                                                    <  2:1697631/149‑1 (MQ=255)

                         tactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCCCCCTCGATAAATCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGttt                                                                                                                    <  1:1183074/149‑1 (MQ=39)

                         tactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGATAATTGCTGAAAAACGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGttt                                                                                                                    >  2:917833/1‑149 (MQ=255)

                           ctTCAAGCTCAGCAGCTTGACCTTCTTCTAAGGATTTGTAACCAACTTGGTTAAGGGCTTAAAAATTTACGAATACGTCGTTTTCTGCTTCGACTTCGATAAAGCCGTATCCTTTTT‑AGCGTTAAACCAGTTAACTGTACCTTGTTTCa                                                                                                                  <  2:643392/149‑1 (MQ=255)

                               aaaCTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAAt                                                                                                              >  2:1670547/1‑149 (MQ=255)

                               aaaCTCAACAGCTTGACCTTCTTCTAATGATGTGTAACCATCTTTGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAAt                                                                                                              <  2:1184044/149‑1 (MQ=255)

                                taCTCACCAGCTTGACCTTCTTCTAACGATTTTTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc                                                                                                             <  2:129161/148‑1 (MQ=255)

                                  cTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCGTTTTT‑AGCGTTAAACAATTTAACTGTACCTTGTTTCATAATCTg                                                                                                           >  2:1308641/1‑149 (MQ=255)

                                       cAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGACTACGTCCTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTGCATAATCGGAAAcc                                                                                                      >  2:391143/1‑149 (MQ=38)

                                        aGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCt                                                                                                     >  1:530291/1‑149 (MQ=255)

                                        aGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCt                                                                                                     >  1:1141381/1‑149 (MQ=255)

                                         gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACGGTACCTTGTTTCATAATCTGAAACCTc                                                                                                    >  1:641989/1‑149 (MQ=255)

                                           ttGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCa                                                                                                  <  2:595861/149‑1 (MQ=255)

                                            tGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCaa                                                                                                 >  1:592298/1‑149 (MQ=255)

                                              aCCTTCTTCTAATGATTTGTAACCATCTAGGTTAATTGCTGAAAAATGTACGTATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCATGTT‑AGCGTTAAACCATTTAAATGTACCTTGTTTCATAATCTGAAACCTCCaaaa                                                                                               >  2:946962/1‑147 (MQ=255)

                                                 ttcttcTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTa                                                                                            >  1:616360/1‑149 (MQ=255)

                                                 ttcttcTAATGATTTGTAACCATCTTGGCTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTAT‑TGCGTTAAACCATTTAACTGGACCTTGTTTCATAATCTGAAACCTCCAAGACTa                                                                                            >  2:944734/1‑149 (MQ=255)

                                                  tcttctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTaa                                                                                           >  2:1563277/1‑149 (MQ=255)

                                                  tcttctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTaa                                                                                           <  1:1308347/149‑1 (MQ=255)

                                                     tctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAat                                                                                        <  1:78336/149‑1 (MQ=255)

                                                       tAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCCTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTATTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAatcc                                                                                      >  1:1161165/1‑147 (MQ=255)

                                                         aTGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcat                                                                                    >  1:383461/1‑149 (MQ=255)

                                                          tGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTTCTTCATCTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCACCAAAACTAAAattcatt                                                                                   >  2:1503006/1‑149 (MQ=255)

                                                          tGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcatt                                                                                   <  2:1335874/149‑1 (MQ=255)

                                                          tGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcatt                                                                                   >  2:1298451/1‑149 (MQ=255)

                                                           gATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcattc                                                                                  >  1:215352/1‑149 (MQ=255)

                                                           gATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcattc                                                                                  >  1:1152809/1‑149 (MQ=255)

                                                           gATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTAGATAAAGCCGAATCCTGTTT‑AGCGTTAGACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcattc                                                                                  >  2:966391/1‑149 (MQ=255)

                                                            aTTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAAttcattca                                                                                 >  2:1319262/1‑149 (MQ=255)

                                                            aTTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAAttcattca                                                                                 >  1:1492680/1‑149 (MQ=255)

                                                                 tAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATg                                                                            <  2:1071247/149‑1 (MQ=255)

                                                                  aaCCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGc                                                                           <  2:1248565/149‑1 (MQ=255)

                                                                     cATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCttt                                                                        >  1:922138/1‑148 (MQ=255)

                                                                       tCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTAtt                                                                      <  2:1492694/149‑1 (MQ=255)

                                                                        cTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTc                                                                     <  2:616360/149‑1 (MQ=255)

                                                                         tttgTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCg                                                                    <  1:1659694/146‑1 (MQ=255)

                                                                         ttGGTTAATTGCTGAAAAATGTACGAATTCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCg                                                                    <  1:1698659/149‑1 (MQ=255)

                                                                         ttGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCg                                                                    <  2:1609452/149‑1 (MQ=255)

                                                                          tGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGc                                                                   <  1:1328545/149‑1 (MQ=255)

                                                                          tGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGc                                                                   <  1:1439544/149‑1 (MQ=255)

                                                                           ggTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGcc                                                                  >  1:616403/1‑148 (MQ=255)

                                                                           ggTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCa                                                                  >  2:1505902/1‑149 (MQ=255)

                                                                           ggTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCa                                                                  <  1:267713/149‑1 (MQ=255)

                                                                            gTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCat                                                                 <  1:1379312/149‑1 (MQ=255)

                                                                              tacttGCTGAAAAATGGACGGATACGCCATTTTCTCCTCCAACTTCGATAAACCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCatat                                                               <  1:46828/146‑1 (MQ=255)

                                                                                  tGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACa                                                           <  2:564944/149‑1 (MQ=255)

                                                                                  tGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACa                                                           >  2:180476/1‑149 (MQ=255)

                                                                                   gCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCTAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaa                                                          <  1:742180/149‑1 (MQ=255)

                                                                                     tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTACACCATTGAACTGTACCTTGTTTCATAATCTGAAACCTCCAGGACTAAAATTCATTCAATATGCTTATTCGCACATTACaaaa                                                        >  2:1058868/1‑149 (MQ=255)

                                                                                     tGAAAAATGTACGAATACGTCATTTTCTACTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGGACCTTGTTTCATAATCTGAAACCACCAAGACTAAAAGTCATTCAATATGCTTAGTCGCACATTACaaag                                                        >  1:1207979/1‑148 (MQ=255)

                                                                                      gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaaaa                                                       <  2:1321239/149‑1 (MQ=255)

                                                                                          aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATAc                                                   <  2:953495/149‑1 (MQ=255)

                                                                                          aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATAc                                                   <  1:523702/149‑1 (MQ=255)

                                                                                                  aaTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAAt                                           >  1:1301955/1‑149 (MQ=255)

                                                                                                      cGTCAGTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACATCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCa                                       <  2:1254005/149‑1 (MQ=255)

                                                                                                       gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCAc                                      <  1:441289/149‑1 (MQ=255)

                                                                                                       ctCATTTTCTCCTTCAACTTCGACAAAGCCGAATCCTTTTT‑AGCGTTAAAACGTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCAc                                      <  1:48217/148‑1 (MQ=255)

                                                                                                                tcCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATAtt                             <  1:140570/149‑1 (MQ=255)

                                                                                                                tcCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATAtt                             <  1:581694/149‑1 (MQ=255)

                                                                                                                  cgtCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                           <  2:456626/147‑1 (MQ=255)

                                                                                                                  cTTCAACTTCGATAACGCTGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCCCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                           <  2:2214/149‑1 (MQ=255)

                                                                                                                  cTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTCACTGTTCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCATTATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                           <  1:26808/149‑1 (MQ=255)

                                                                                                                  cTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                           <  2:1058874/149‑1 (MQ=255)

                                                                                                                  cTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                           <  2:1707984/149‑1 (MQ=255)

                                                                                                                  cTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATGTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAGAAAAAATACATGCAAATTTCACTCAAATATTCt                           <  1:413170/149‑1 (MQ=255)

                                                                                                                   ttCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAATCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAACACATGCAAATTTCACTCAAATATTCtt                          <  1:917833/149‑1 (MQ=255)

                                                                                                                   ttCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                          >  1:914733/1‑149 (MQ=255)

                                                                                                                        cTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCaa                     <  1:1624750/149‑1 (MQ=255)

                                                                                                                        cTTCGATAAAGCCCATTCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCaa                     <  1:1504777/149‑1 (MQ=255)

                                                                                                                           tgagaaaGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAACCCTCCAAGACTAAAATTCATTCACTATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                  <  2:256902/145‑1 (MQ=255)

                                                                                                                           cGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                  <  1:292266/149‑1 (MQ=255)

                                                                                                                           cGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                  <  1:464710/149‑1 (MQ=255)

                                                                                                                           cGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGGTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                  <  2:1335615/149‑1 (MQ=255)

                                                                                                                           cGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATCTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                  <  1:433808/149‑1 (MQ=255)

                                                                                                                            gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGGTTCATAATCTGAAACCTCCAAGACTAAACTTCATTGATTATGCTTCTTCCACTATTAGAAAAAATACATGCAAATTTCACTCAAATATTCTTTGACATATg                 >  2:502510/1‑149 (MQ=255)

                                                                                                                             aTAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg                <  1:80053/149‑1 (MQ=255)

                                                                                                                                 aGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATTTGGaata            >  1:1321738/1‑149 (MQ=255)

                                                                                                                                 aGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaata            <  2:1351697/149‑1 (MQ=255)

                                                                                                                                 aGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCAAATTATAAATATTGCTGGCAAATTTCACTCAAATATTCTTTGCAATATGGaata            >  1:131476/1‑149 (MQ=255)

                                                                                                                                   ccGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAACCTACAGGCAAATTTCACTCAAATATTCTTTGCAATATGGaataat          >  1:1327169/1‑149 (MQ=255)

                                                                                                                                   ccGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataat          >  2:1352278/1‑149 (MQ=255)

                                                                                                                                      aaTCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat       >  1:891204/1‑149 (MQ=255)

                                                                                                                                      aaTCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat       >  1:106559/1‑149 (MQ=255)

                                                                                                                                           cttttTAACGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAGAATCATCTGc   <  2:1055886/148‑1 (MQ=255)

                                                                                                                                            ttttTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt  <  1:1491716/149‑1 (MQ=255)

CTTGTGGACCGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCT  >  USA300TCH1516_ALE/1439863‑1440151

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`