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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,073,225 T→C W563R (TGG→CGG)  flu → CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,073,2250TC100.0% 680.6 / NA 183W563R (TGG→CGG) fluCP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (79/104);  total (79/104)

Only 100 of 184 total aligned reads displayed.

ACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGA  >  NC_000913/2073090‑2073356
                                                                                                                                       |                                                                                                                                   
 cgctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCTGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGaa                                                                                                                                 <  1:212992/139‑1 (MQ=255)
 cgctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGaa                                                                                                                                 >  1:121856/1‑139 (MQ=255)
   ctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTTAAGCTGAGCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCCCCCGGaaaa                                                                                                                               >  2:605405/1‑137 (MQ=255)
        gctgaACGACAGTACCGTCA‑CACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCg                                                                                                                         >  2:1027750/1‑139 (MQ=255)
          tgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGa                                                                                                                        <  1:139381/139‑1 (MQ=255)
           gaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGAt                                                                                                                       <  2:883110/139‑1 (MQ=255)
                  aGTACCGTCACGACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGTTAACGCCa                                                                                                                <  1:854286/139‑1 (MQ=255)
                  aGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCa                                                                                                                <  1:607104/139‑1 (MQ=255)
                   gTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCAc                                                                                                               <  1:1073295/139‑1 (MQ=255)
                      ccGTCA‑CACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTg                                                                                                           <  1:1027750/139‑1 (MQ=255)
                           accacGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGt                                                                                                       <  1:807773/139‑1 (MQ=255)
                           accacGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGt                                                                                                       <  2:728443/139‑1 (MQ=255)
                            ccacGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCGCGGTGCAGTc                                                                                                      <  2:886728/139‑1 (MQ=255)
                            ccacGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTc                                                                                                      >  2:243984/1‑139 (MQ=255)
                              acGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGa                                                                                                                                  >  1:1243430/1‑109 (MQ=255)
                              acGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGa                                                                                                                                  <  2:1243430/109‑1 (MQ=255)
                                    gTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGtggtgg                                                                                              >  1:430882/1‑139 (MQ=255)
                                     tCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             <  1:176414/139‑1 (MQ=255)
                                     tCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             <  1:1300812/139‑1 (MQ=255)
                                         tGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGAc                                                                                         >  1:1308585/1‑139 (MQ=255)
                                            tCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             <  1:273242/132‑1 (MQ=255)
                                            tCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTc                                                                                      >  2:230822/1‑139 (MQ=255)
                                              aGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAg                                                                                    <  2:83244/139‑1 (MQ=255)
                                              aGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAg                                                                                    <  1:1096187/139‑1 (MQ=255)
                                              aGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGCCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAg                                                                                    >  1:1102759/1‑139 (MQ=255)
                                                cgcgGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCATGGTGCAGTCGGTGGTGGATGACCTCAg                                                                                    <  1:734522/137‑1 (MQ=255)
                                                cgcgGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAg                                                                                    >  2:734522/1‑137 (MQ=255)
                                                cgcgGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGcc                                                                                  >  1:1047373/1‑139 (MQ=255)
                                                cgcgGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGcc                                                                                  <  2:1047373/139‑1 (MQ=255)
                                                cgcgGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGcc                                                                                  <  2:644061/139‑1 (MQ=255)
                                                   ggTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATg                                                                               <  2:288514/139‑1 (MQ=255)
                                                     tACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGcc                                                                             >  1:825400/1‑139 (MQ=255)
                                                     tACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGcc                                                                             >  1:1185436/1‑139 (MQ=255)
                                                          cccTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACa                                                                        >  2:684682/1‑139 (MQ=255)
                                                          cccTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACa                                                                        >  1:1062571/1‑139 (MQ=255)
                                                          cccTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGAACTCAGCCATGCCGGACa                                                                        >  1:418185/1‑139 (MQ=255)
                                                             tGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCa                                                                                                                <  1:423254/96‑1 (MQ=255)
                                                              gAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGAtt                                                                    <  2:181117/139‑1 (MQ=255)
                                                              gAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGAtt                                                                    <  2:737980/139‑1 (MQ=255)
                                                               aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCggtg                                                                                                  <  2:169016/108‑1 (MQ=255)
                                                               aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGAt                                                                                            >  1:432056/1‑114 (MQ=255)
                                                               aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGAt                                                                                            <  2:432056/114‑1 (MQ=255)
                                                               aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTc                                                                   >  2:1086467/1‑139 (MQ=255)
                                                               aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTc                                                                   >  2:341880/1‑139 (MQ=255)
                                                               aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTc                                                                   >  1:323572/1‑139 (MQ=255)
                                                                    gACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGaa                                                                                                                                 >  2:1195728/1‑72 (MQ=255)
                                                                    gACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGaa                                                                                                                                 <  1:1195728/72‑1 (MQ=255)
                                                                    gACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAg                                                                                    >  1:953943/1‑117 (MQ=255)
                                                                       cGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCAcc                                                           <  1:684682/139‑1 (MQ=255)
                                                                           agcaCTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCa                                                       <  1:1043273/139‑1 (MQ=255)
                                                                            gcaCTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      <  2:786647/139‑1 (MQ=255)
                                                                            gcaCTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      <  2:1310076/139‑1 (MQ=255)
                                                                            gcaCTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      <  1:663428/139‑1 (MQ=255)
                                                                            gcaCTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      <  2:1102759/139‑1 (MQ=255)
                                                                            gcaCTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTACGGTGCCACCCGGAATAGACCCGATAAAGCCACGGTTCAGTCGGTGGTGGACGACGTCAGCCATGCCGGACAGATTCATTTCACCTGCAc                                                      <  2:953885/139‑1 (MQ=255)
                                                                              aCTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAccc                                                    <  2:961313/139‑1 (MQ=255)
                                                                               cTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCg                                                   <  1:1086467/139‑1 (MQ=255)
                                                                                 gtgCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGca                                                 <  1:341880/139‑1 (MQ=255)
                                                                                      gAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAggg                                            <  1:1017872/139‑1 (MQ=255)
                                                                                       aaCGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTcc                                                        <  1:1277822/126‑1 (MQ=255)
                                                                                       aaCGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTcc                                                        >  2:1277822/1‑126 (MQ=255)
                                                                                          ggTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCggtg                                                                                                  <  1:161831/81‑1 (MQ=255)
                                                                                            tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             >  2:42793/1‑84 (MQ=255)
                                                                                            tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             >  1:1080752/1‑84 (MQ=255)
                                                                                            tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      <  2:48985/123‑1 (MQ=255)
                                                                                            tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      >  1:48985/1‑123 (MQ=255)
                                                                                            tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTc                                      >  2:853375/1‑139 (MQ=255)
                                                                                              ccATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGt                                    >  2:126195/1‑139 (MQ=255)
                                                                                                aTTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTAc                                  <  2:121856/139‑1 (MQ=255)
                                                                                                    aCCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTg                                                                                                           <  2:636054/62‑1 (MQ=255)
                                                                                                    aCCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTg                                                                                                           >  1:636054/1‑62 (MQ=255)
                                                                                                    aCCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGc                              <  1:1255311/139‑1 (MQ=255)
                                                                                                      cccACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATc                                                                                                                             >  2:1135847/1‑42 (MQ=255)
                                                                                                      cccACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATc                                                                                                                             <  1:1135847/42‑1 (MQ=255)
                                                                                                      cccACGAATGTCACTCTCGCCGCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGAGAAGTTCGTACCGGCaa                            <  1:1299477/139‑1 (MQ=255)
                                                                                                             aTGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGaa                     <  2:1304766/139‑1 (MQ=255)
                                                                                                              tGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGaaa                    >  2:1021033/1‑139 (MQ=255)
                                                                                                                tCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCAtt                                                                >  1:679707/1‑93 (MQ=255)
                                                                                                                tCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCAcc                                                           <  1:886151/98‑1 (MQ=255)
                                                                                                                   ctctCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGaa               >  2:302773/1‑139 (MQ=255)
                                                                                                                   ctctCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGaa               >  2:1081251/1‑139 (MQ=255)
                                                                                                                    tctcGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGtggtgg                                                                                              >  2:1141394/1‑59 (MQ=255)
                                                                                                                     ctcGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      >  2:392739/1‑98 (MQ=255)
                                                                                                                     ctcGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      <  1:392739/98‑1 (MQ=255)
                                                                                                                      tcGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGa                                           >  2:906330/1‑108 (MQ=255)
                                                                                                                      tcGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGa                                           <  1:906330/108‑1 (MQ=255)
                                                                                                                       cGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAAc           >  1:1142368/1‑139 (MQ=255)
                                                                                                                       cGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAAc           >  1:35705/1‑139 (MQ=255)
                                                                                                                         ccTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGc                              <  2:672283/118‑1 (MQ=255)
                                                                                                                         ccTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCt         >  2:387814/1‑139 (MQ=255)
                                                                                                                         ccTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCt         >  2:1074167/1‑139 (MQ=255)
                                                                                                                          cTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGc                                                  >  1:889613/1‑97 (MQ=255)
                                                                                                                          cTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGc                                                  <  2:889613/97‑1 (MQ=255)
                                                                                                                          cTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTg        >  1:788490/1‑139 (MQ=255)
                                                                                                                           tCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCgg                                                                           >  1:239858/1‑71 (MQ=255)
                                                                                                                           tCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa       <  2:882959/139‑1 (MQ=255)
                                                                                                                              ggTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACg    <  2:418185/139‑1 (MQ=255)
                                                                                                                                tGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGa  <  2:1062571/139‑1 (MQ=255)
                                                                                                                                  ccACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             >  2:51433/1‑46 (MQ=255)
                                                                                                                                  ccACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             <  1:51433/46‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                   
ACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGA  >  NC_000913/2073090‑2073356

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A