Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,210,488 C→T 9.1% S799S (AGC→AGT)  PP_3692 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,210,4880CT 9.1% 113.4 / 3.0 45S799S (AGC→AGT) PP_3692hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/17);  new base T (2/2);  total (26/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.60e-01

CCGGACTCGTGGCGAACCAAAATGCCCGCGACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCAAAGTCACGGTTGAGGACTGCATGTTCATTGACGATCTG  >  NC_002947/4210340‑4210635
                                                                                                                                                    |                                                                                                                                                   
ccGGACTCGTGGCGAACCAAAATGCCCGCGACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCg                                                                                                                                                    <  2:1846730/150‑1 (MQ=255)
    aCTCGTGGCGAACCAAAATGCCCGCGACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGAttt                                                                                                                                                >  1:1762565/1‑150 (MQ=255)
        gTGGCGAACCAAAATGCCCGCGACGCCAAACCAGCCATCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAgg                                                                                                                                            <  1:1092684/150‑1 (MQ=255)
        gTGGCGAACCAAAATGCCCGCGACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAgg                                                                                                                                            >  2:363209/1‑150 (MQ=255)
                         ccGCGACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAAc                                                                                                                           >  1:1702542/1‑150 (MQ=255)
                           gcgACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCg                                                                                                                         >  1:1171923/1‑150 (MQ=255)
                             gACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGtt                                                                                                                       <  1:1242134/150‑1 (MQ=255)
                             gACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGtt                                                                                                                       <  2:1762565/150‑1 (MQ=255)
                             gACGCCAAACCAGCCAGCGGGGTAAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGtt                                                                                                                       <  2:480635/150‑1 (MQ=255)
                                gCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGTGATTTCa                                                                                                                                              <  1:474548/124‑1 (MQ=255)
                                gCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGTGATTTCa                                                                                                                                              <  1:473482/124‑1 (MQ=255)
                                gCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGTGATTTCa                                                                                                                                              >  2:474548/1‑124 (MQ=255)
                                gCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGTGATTTCa                                                                                                                                              >  2:473482/1‑124 (MQ=255)
                                 ccAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGt                                                                                                                   <  2:1065526/150‑1 (MQ=255)
                                   aaaCCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGAGGAAAAAACCGTTGAGTTc                                                                                                                 >  2:1274299/1‑150 (MQ=255)
                                   aaaCCAGCCAGCGGGGTCAAATACCTGATCGACCACACGAACAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTc                                                                                                                 >  1:1850422/1‑150 (MQ=255)
                                    aaCCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCa                                                                                                                <  1:1157745/150‑1 (MQ=255)
                                            agcGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTctgctg                                                                                                        >  1:481815/1‑150 (MQ=255)
                                            agcGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAACCCTTCCATGGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCGTTctgctg                                                                                                        >  1:1088440/1‑150 (MQ=255)
                                                   tCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATg                                                                                                 <  2:1171923/150‑1 (MQ=255)
                                                           cTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGc                                                                                         >  2:983435/1‑150 (MQ=255)
                                                            tGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTctg                                                                                                           <  1:1156234/131‑1 (MQ=255)
                                                            tGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTctg                                                                                                           >  2:1156234/1‑131 (MQ=255)
                                                                 gACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGGAAAAACCGTTGAGTTAATTCTGCTGGCTGATGTCGTAGGCCGCTTc                                                                                   >  2:840107/1‑150 (MQ=255)
                                                                  aCCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTcc                                                                                  >  2:1613104/1‑150 (MQ=255)
                                                                             aaGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGcactc                                                                       >  1:836956/1‑150 (MQ=255)
                                                                             aaGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCAACCCACTGGCTGATGTCGTAGGCCGCTTCCGCCGTGcaatc                                                                       >  1:100467/1‑150 (MQ=255)
                                                                                      aagaacCACCAGGGAAACGGTGAAGTAGGTAACAACTAAGGCATTGGAAAAAGCGCTTGAAGCGATTTGAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAg                                                              <  2:100467/150‑1 (MQ=255)
                                                                                              ccAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCt                                                      >  2:600874/1‑150 (MQ=255)
                                                                                                    aaaCGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTgctgg                                                                                                       >  2:122519/1‑95 (MQ=255)
                                                                                                    aaaCGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTgctgg                                                                                                       <  1:122519/95‑1 (MQ=255)
                                                                                                                cGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCAAAGt                                    <  2:481815/150‑1 (MQ=255)
                                                                                                                       tACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTgctggc                                                                                                      <  2:1324564/77‑1 (MQ=255)
                                                                                                                       tACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTgctggc                                                                                                      >  1:1324564/1‑77 (MQ=255)
                                                                                                                       tACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCAAAGTCACGGtt                             >  1:1685664/1‑150 (MQ=255)
                                                                                                                       tACGAAGTGATGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCg                                                                                       >  1:5842/1‑92 (MQ=255)
                                                                                                                       tACGAAGTGATGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCg                                                                                       <  2:5842/92‑1 (MQ=255)
                                                                                                                           aaGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCAAAGTCACGGTTGAgg                         >  1:505294/1‑150 (MQ=255)
                                                                                                                                cgggggAAAAGCGCCTGCAGCGATTTCATGAGCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCAAAGTCACGGTTGAGGACTGc                    <  2:836956/148‑1 (MQ=255)
                                                                                                                                            gcTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCAAAGTCACGGTTGAGGACTGCATGTTCATTGAc        >  1:1587175/1‑150 (MQ=255)
                                                                                                                                                  aGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCAtt                                                                                                              >  1:434688/1‑42 (MQ=255)
                                                                                                                                                  aGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCAtt                                                                                                              <  2:434688/42‑1 (MQ=255)
                                                                                                                                                  aGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCAAAGTCACGGTTGAGGACTGCATGTTCATTGACGATCtg  >  1:788480/1‑150 (MQ=255)
                                                                                                                                                   gCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCaaa                                      <  2:368622/113‑1 (MQ=255)
                                                                                                                                                   gCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCaaa                                      >  1:368622/1‑113 (MQ=255)
                                                                                                                                                    |                                                                                                                                                   
CCGGACTCGTGGCGAACCAAAATGCCCGCGACGCCAAACCAGCCAGCGGGGTCAAATACCTGATCGACCACACGATCAAGCACCTGAAGAAGCACCAGGAAAACGGTGAAGTCGATAACTACGAAGTGCTGGGCAAAAGCGCTTGCAGCGATTTCAGGATCATCGTGGAAAAAACCGTTGAGTTCATTCTGCTGGCTGATGTCGTAGGCCGCTTCCGCCGTGCAATCAATACTCAGGGCAAGCTGCATAAGGTTGCCAAAGTCACGGTTGAGGACTGCATGTTCATTGACGATCTG  >  NC_002947/4210340‑4210635

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑