Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,797,772	G→C	R7G (CGC→GGC)	phoR ←	Alkaline phosphatase synthesis sensor protein PhoR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,797,772	0	G	C	100.0%	272.7 / NA	80	R7G (CGC→GGC)	phoR	Alkaline phosphatase synthesis sensor protein PhoR
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (36/44);  total (36/44)

TAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTCT  >  USA300TCH1516_ALE/1797636‑1797909                                                                                                                                         |                                                                                                                                          taaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCcgtgg                                                                                                                                       <  1:551399/141‑1 (MQ=255)  aaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCGATAACATTAAGCcgtggg                                                                                                                                      >  1:862328/1‑140 (MQ=255)   aataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCgtggtg                                                                                                                                     <  1:649508/141‑1 (MQ=255)       tatGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAAc                                                                                                                                 <  1:1040523/141‑1 (MQ=255)          gATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtc                                                                                                                              <  1:412733/141‑1 (MQ=255)           ttCTTGCATCTGTTGCTAGAGCTTGTCCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtca                                                                                                                             <  2:1028685/140‑1 (MQ=255)               tGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATAAATAACATTAAGCCGTGGTGAAACTTcataat                                                                                                                         >  2:594823/1‑141 (MQ=255)                  aTCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGt                                                                                                                      >  1:42481/1‑141 (MQ=255)                   tCTGTTGCTAGAGCTTGTTCGTGTTTTTTTTTTTTTTTTTATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACGAAACTGATAATTAATCTATTGCTTATCAATAATATTAATCCGTGGTGAAACTTCATCCTtttt                                                                                                                     >  2:410507/1‑141 (MQ=255)                   tCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGtt                                                                                                                     >  1:1036337/1‑141 (MQ=255)                   tCTGGTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGtt                                                                                                                     <  1:432166/141‑1 (MQ=255)                      gTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCtt                                                                                                                  <  1:684445/141‑1 (MQ=255)                       ttGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGTTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTAttt                                                                                                                 >  2:909073/1‑141 (MQ=255)                       ttGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCttt                                                                                                                 <  2:764685/141‑1 (MQ=255)                         tcTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAg                                                                                                               <  2:999900/140‑1 (MQ=255)                         gCTAGAGCTTGTTCGTGTTTTTTTTTTTTATTTTATGTGATGGAAGCGTGAATAATAATGCCTAATGTAAGAAAACTGATAATGAATATACCGCTTATCAATAACATTAAGCCGTGGTGAAACTTCGTCTTTGTTGTTTat                                                                                                               >  2:610560/1‑140 (MQ=255)                             gagCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCt                                                                                                           <  2:42481/141‑1 (MQ=255)                             gagCTTGTTAGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGCGGTTAAACGGCATCATTGTTCTTTAGGTCt                                                                                                           <  1:1198579/141‑1 (MQ=255)                                 ttGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATACTCCTACTTAATGGAACAAAACTGATAATTAATATACTGCTTAACAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTcc                                                                                                       <  1:935008/141‑1 (MQ=255)                                   gTTCGTGTTTTTCTGATAAAACATATGTGATGGAATCGTGAATAATAATGCCTAATTTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCaa                                                                                                     <  1:1195212/141‑1 (MQ=255)                                   gTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCaa                                                                                                     >  1:970503/1‑141 (MQ=255)                                   gTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATAATTGTTCTTTAAGTCTTTCCaa                                                                                                     >  1:510953/1‑141 (MQ=255)                                     tCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAGCTTCATCATTGTTCTTTAGGTCTTTCCAAtt                                                                                                   >  1:247244/1‑141 (MQ=255)                                            tttCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGcc                                                                                            <  1:878847/141‑1 (MQ=255)                                               cTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTaa                                                                                         <  1:712137/141‑1 (MQ=255)                                                 gATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGc                                                                                       <  2:651654/141‑1 (MQ=255)                                                     aaaCATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACg                                                                                   >  1:781441/1‑141 (MQ=255)                                                       aCAAATGAGATGGAAGCGGGAAAAATAAAGGCTAATGTAACAAAACTGATAATTAATATACTGCCTATCAACAACATTAAGCCGTGGTGAAACCTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGca                                                                                 <  1:36918/141‑1 (MQ=255)                                                                 tGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTCATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaat                                                                       <  1:858191/141‑1 (MQ=255)                                                                 tGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaat                                                                       <  1:956168/141‑1 (MQ=255)                                                                  ggAAGCGTGAATAATGATGCCTAATGTAACAAAAATGATAATTAATATACTGCTTAGCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCAGAGTTTtaata                                                                      >  2:617476/1‑141 (MQ=255)                                                                     aGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                   >  1:309241/1‑141 (MQ=255)                                                                      gcctGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                  <  1:1107673/138‑1 (MQ=255)                                                                      gCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCTTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                  <  1:878134/141‑1 (MQ=255)                                                                      gCGTGAACAATAATGCCTAATGTAACAAAACTGATAATTAATATACGGATTATCAATAACAATAGGCCGAGGGGCGAATACAACAGTGTATATCAGGTCGTTACAATTCATATCCTACAACACGCCCAGTTTTATTAAGtt                                                                  >  2:95163/1‑141 (MQ=255)                                                                       cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                                 >  1:673548/1‑141 (MQ=255)                                                                       cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                                 >  2:367223/1‑141 (MQ=255)                                                                       cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATGTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                                 >  2:1026964/1‑141 (MQ=255)                                                                           aataataatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGc                                                             <  1:385052/141‑1 (MQ=255)                                                                               ataatGCCTTATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTAATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGcttct                                                         <  1:825044/141‑1 (MQ=255)                                                                                taatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGcttctt                                                        <  1:646311/141‑1 (MQ=255)                                                                                 aatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTAGAGCCTAAGCCACGAACAGTTTTAATAAGTTGTGGCTTCTTa                                                       >  2:486719/1‑141 (MQ=255)                                                                                  atGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAg                                                      >  2:1178250/1‑141 (MQ=255)                                                                                  atGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAg                                                      >  2:1056177/1‑141 (MQ=255)                                                                                   tGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAgg                                                     <  2:386872/141‑1 (MQ=255)                                                                                   ctccTAATGTAACAAAACTGACAATTAACATACTTCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAgg                                                     <  1:250511/139‑1 (MQ=255)                                                                                    tccTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGa                                                    <  2:713038/140‑1 (MQ=255)                                                                                    gCCTAATGTAACAAAACTGATAATTAATATCCTGCTTATCAATAACATTAAGACGTGGTGAAACTTCAACATTTTTCTTTTGGTCTTTCCGATGTCGAGCCTAAGCCACGCACAGTTTTACTACGTTGTGGTTTCTTAgca                                                    <  2:528018/141‑3 (MQ=255)                                                                                       tAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTa                                                 >  1:1166200/1‑141 (MQ=255)                                                                                       tAATGTAAAAAAACTGATAATTATTATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCAGTATTGTTCTTTTGGTCATTTCAATTTGAATCCTGAGCCTCTCACAGTTTTAATAAGTTGTGTCTTCGTTGGATTa                                                 <  2:378028/141‑1 (MQ=255)                                                                                        aaTGTAACAAAACTGATAATTAATATACTGCTTATCAATATCATGAAGCCGTGGTGAAACTTCTTCATTGTTCTGTAGGTATTTACAATTTGTCGCCTAAGTCACGTACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAt                                                <  2:1052466/141‑1 (MQ=255)                                                                                        aaTGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAt                                                <  1:580121/141‑1 (MQ=255)                                                                                          tGTAACAAACCTGATAACTAACACCCCGGTTATCATGACCATTAATCCGTGGTGAAACTTCATCATTGTTCTTAATATCTTTCCAATTTATAGCATAAGCCTCGCACAGTTTTAATAAGCTCTCGCTTCTTAGGATTAtac                                              <  2:499230/141‑3 (MQ=255)                                                                                          tGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtct                                              <  1:410507/141‑1 (MQ=255)                                                                                             aaCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtcttct                                           >  1:1009351/1‑141 (MQ=255)                                                                                             aaCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtcttct                                           <  1:210238/141‑1 (MQ=255)                                                                                             aaCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtcttct                                           <  1:130393/141‑1 (MQ=255)                                                                                                aaaaCTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAAt                                        <  2:904809/141‑1 (MQ=255)                                                                                                    cTGATAATTAATATACTGGTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTCTAGGTCTTTCCAATTTATAGCCTAAGCAACGCACAGTTTTAATAAATTGTGGCTTCTTAGGATTATCTTCTAATTTAt                                    >  2:695381/1‑141 (MQ=255)                                                                                                       aTAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtctc                                 <  1:631450/141‑1 (MQ=255)                                                                                                         aattaatATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTACGCCACGCACAGTTTTAATAAGTTTTGGCTTCTTAGGATTATCTTCTATTTTCTCTCtt                               >  2:145261/1‑141 (MQ=255)                                                                                                           ttaatATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTaa                             <  1:950616/141‑1 (MQ=255)                                                                                                                    tGCTTATCAATAACATTAAGCCGTGGTGAAACCTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTTATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGat                    <  1:805598/141‑1 (MQ=255)                                                                                                                     tcTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTACAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGata                   <  2:834340/140‑1 (MQ=255)                                                                                                                     gCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGata                   <  2:565822/141‑1 (MQ=255)                                                                                                                      tttATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGatat                  <  2:398922/140‑1 (MQ=255)                                                                                                                      cTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGatat                  <  2:747753/141‑1 (MQ=255)                                                                                                                      cTTAACAATAACATTAAGCCGTGGTGAAACTCCATCGTTATTCCTTTTGTCTTTACAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAACTGACCGatat                  <  2:543225/141‑1 (MQ=255)                                                                                                                         aTCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTCAGCCACGCACAGTTTTAATACGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAACTGACTGatctctc               >  2:566461/1‑136 (MQ=255)                                                                                                                         aTCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTa               >  2:437888/1‑141 (MQ=255)                                                                                                                          tCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATCGCCTAAGAAACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGCTTACGTTCTAATTTATTTCTTAAATGACTGTTATGTAc              >  2:829104/1‑141 (MQ=255)                                                                                                                          tCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTAc              >  2:883651/1‑141 (MQ=255)                                                                                                                           gaaTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTGCAATTTATAGCCTAAGCCAAGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATATTCTAATTTATATCTTAAATGACTGATATGTCCa             >  2:668948/2‑141 (MQ=255)                                                                                                                           cAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCATAAATGACTGAGATGTaaa             >  1:349323/1‑139 (MQ=255)                                                                                                                            aaTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACAt            >  1:901359/1‑141 (MQ=255)                                                                                                                             aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATc           >  2:450346/1‑141 (MQ=255)                                                                                                                                  aTTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaccaa      >  2:271850/1‑141 (MQ=255)                                                                                                                                  aTTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaacaa      >  1:166905/1‑141 (MQ=255)                                                                                                                                  aTTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaacaa      >  2:1054217/1‑141 (MQ=255)                                                                                                                                  aTTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCGCTTAAATGACTGATATGTACATcaacaa      >  1:838035/1‑141 (MQ=255)                                                                                                                                      aGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTTTCTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTCt  <  2:656564/141‑1 (MQ=255)                                                                                                                                      aGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTCt  >  2:375574/1‑141 (MQ=255)                                                                                                                                         |                                                                                                                                          TAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTCT  >  USA300TCH1516_ALE/1797636‑1797909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑