Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,458,420 T→A 13.5% Y28N (TAT→AAT)  gspE → general secretory pathway component, cryptic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,458,4200TA13.5% 157.0 / 15.1 52Y28N (TAT→AAT) gspEgeneral secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base T (23/22);  new base A (3/4);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGAT  >  NC_000913/3458294‑3458565
                                                                                                                              |                                                                                                                                                 
ttCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGAttattta                                                                                                                                                  <  2:768664/128‑1 (MQ=255)
ttCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGAttattta                                                                                                                                                  >  1:768664/1‑128 (MQ=255)
    aCAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGa                                                                                                                             >  4:387257/1‑145 (MQ=255)
    aCAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGa                                                                                                                             <  3:387257/145‑1 (MQ=255)
                       aTCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGAttattt                                                                                                                                                   >  3:418089/1‑104 (MQ=255)
                       aTCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGAttattt                                                                                                                                                   <  4:418089/104‑1 (MQ=255)
                                      cATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGc                                                                                        >  1:1058794/1‑148 (MQ=255)
                                            tatGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGAcc                                                                                  >  1:431221/1‑148 (MQ=255)
                                                  aaTTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAg                                                                                                                            >  3:237384/1‑100 (MQ=255)
                                                  aaTTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAg                                                                                                                            <  4:237384/100‑1 (MQ=255)
                                                  aaTTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGat                                                                                                                <  1:495560/112‑1 (MQ=255)
                                                  aaTTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGAcc                                                                            >  3:1082531/1‑148 (MQ=255)
                                                  aaTTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTAGAGCGGTTACTCGat                                                                                                                >  2:495560/1‑112 (MQ=255)
                                                    ttCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGt                                                                                                       <  4:443854/119‑1 (MQ=255)
                                                    ttCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGt                                                                                                       >  3:443854/1‑119 (MQ=255)
                                                    ttCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAg                                                                          <  2:431221/148‑1 (MQ=255)
                                                     tcactcacCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATAAATAATCTCGc                                                                                                                                            <  3:252642/81‑1 (MQ=255)
                                                     tcactcacCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATAAATAATCTCGc                                                                                                                                            >  4:252642/1‑81 (MQ=255)
                                                       actcacCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCtt                                                                       <  4:1082531/148‑1 (MQ=255)
                                                        ctcacCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCa                                                                                                                                  <  3:225311/88‑1 (MQ=255)
                                                        ctcacCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCa                                                                                                                                  >  4:225311/1‑88 (MQ=255)
                                                         tcacCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGt                                                                     >  1:743507/1‑148 (MQ=255)
                                                            ccGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTc                                                                                                      >  3:323153/1‑112 (MQ=255)
                                                            ccGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTc                                                                                                      <  4:323153/112‑1 (MQ=255)
                                                                    cGCCAGTTGGTCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGt                                                                                          >  3:668429/1‑116 (MQ=255)
                                                                    cGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGt                                                                                          <  4:668429/116‑1 (MQ=255)
                                                                     gCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGAtt                                                         >  2:771728/1‑148 (MQ=255)
                                                                         gTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGa                                                     <  1:771728/148‑1 (MQ=255)
                                                                                     cacaACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCAt                                                                                <  1:313327/109‑1 (MQ=255)
                                                                                     cacaACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCAt                                                                                >  2:313327/1‑109 (MQ=255)
                                                                                         aCGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCg                                                                                                                                          >  3:513865/1‑47 (MQ=255)
                                                                                         aCGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCg                                                                                                                                          <  4:513865/47‑1 (MQ=255)
                                                                                         aCGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGtt                                                                                                 <  1:263658/88‑1 (MQ=255)
                                                                                         aCGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGtt                                                                                                 >  2:263658/1‑88 (MQ=255)
                                                                                         aCGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGa                                                           <  2:829722/126‑1 (MQ=255)
                                                                                         aCGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGa                                                           >  1:829722/1‑126 (MQ=255)
                                                                                         aCGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCg                                     <  2:1058794/148‑1 (MQ=255)
                                                                                                      ctctATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGa                        >  3:479175/1‑148 (MQ=255)
                                                                                                       tctATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGAc                                                                                   <  3:764761/88‑1 (MQ=255)
                                                                                                       tctATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGAc                                                                                   >  4:764761/1‑88 (MQ=255)
                                                                                                        ctATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTggt                                                          <  2:617774/112‑3 (MQ=255)
                                                                                                        ctATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTggt                                                          >  1:617774/1‑110 (MQ=255)
                                                                                                          aTTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATAc                    <  4:479175/148‑1 (MQ=255)
                                                                                                            tCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATg                                                                               <  4:1133525/87‑1 (MQ=255)
                                                                                                            tCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATg                                                                               >  3:1133525/1‑87 (MQ=255)
                                                                                                               gagGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAg                                                                          >  4:148780/1‑89 (MQ=255)
                                                                                                               gagGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAg                                                                          <  3:148780/89‑1 (MQ=255)
                                                                                                                   gCGAGATAAATAATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCgg                 <  1:590546/142‑1 (MQ=255)
                                                                                                                    cGAGATAAATAATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCt                                                 >  3:291291/1‑109 (MQ=255)
                                                                                                                    cGAGATAAATAATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCt                                                 <  4:291291/109‑1 (MQ=255)
                                                                                                                    cGAGATAAATAATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGc                                             >  3:181937/1‑113 (MQ=255)
                                                                                                                    cGAGATAAATAATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGc                                             <  4:181937/113‑1 (MQ=255)
                                                                                                                      agaTTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGa                                                                              <  2:389773/78‑1 (MQ=255)
                                                                                                                      agaTTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGa                                                                              <  2:247688/78‑1 (MQ=255)
                                                                                                                      agaTTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGa                                                                              >  1:389773/1‑78 (MQ=255)
                                                                                                                      agaTTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGa                                                                              >  1:247688/1‑78 (MQ=255)
                                                                                                                         ttatttatCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGa                                         >  2:520303/1‑112 (MQ=255)
                                                                                                                         ttatttatCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGa                                         <  1:520303/112‑1 (MQ=255)
                                                                                                                            tttatCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCgg                                              <  2:895643/104‑1 (MQ=255)
                                                                                                                            tttatCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCgg                                              >  1:895643/1‑104 (MQ=255)
                                                                                                                            tttatCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGAt  <  2:743507/148‑1 (MQ=255)
                                                                                                                              |                                                                                                                                                 
TTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGAT  >  NC_000913/3458294‑3458565

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: