Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,970 T→C 12.5% E194E (GAA→GAG)  tpn ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,9700TC12.5% 98.5 / 7.2 40E194E (GAA→GAG) tpnIS431mec transposase
Reads supporting (aligned to +/- strand):  ref base T (13/22);  new base C (3/2);  total (16/24)
Fisher's exact test for biased strand distribution p-value = 3.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.33e-01

AAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAG  >  CP000730/35837‑36109
                                                                                                                                     |                                                                                                                                           
aacatacAGCTAACCACCAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACACTCCATAc                                                                                                                                      <  2:370553/138‑1 (MQ=1)
                               aGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACt                                                                                                       <  2:500410/141‑1 (MQ=31)
                                gtgtTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACtt                                                                                                      <  1:509724/141‑1 (MQ=32)
                                  gtTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTg                                                                                                    >  2:414274/1‑141 (MQ=32)
                                   ttCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGGGAAAATCCGTAGATCTGAAGAGACCTACGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCCGTATTGATACTTTGa                                                                                                   >  1:606404/1‑141 (MQ=255)
                                   ttCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGa                                                                                                   <  2:13580/141‑1 (MQ=32)
                                           aCTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGt                                                                                           <  1:360687/141‑1 (MQ=32)
                                            gttGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGtc                                                                                          <  2:101350/140‑1 (MQ=17)
                                                 tcgCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGCAGAAACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAATATTCGTTACTGTATTGATACTTTGATGCCTTTtcttttt                                                                                     >  1:211601/3‑139 (MQ=11)
                                                         tgCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACACTCAATAACTTTTCAAGTATTCTTTGCTGTATTGATGCTTTGATGCATTGTCTTTCTTACTTTaa                                                                             >  1:276517/1‑141 (MQ=11)
                                                          gCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAat                                                                            >  2:589603/1‑141 (MQ=35)
                                                            tAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACACTCAATACCTTTTAAAGTATTCGTTGCTGTATTGATACTTGGGTACCTTGTCTTTCTTACTTTAatat                                                                          >  1:277288/1‑141 (MQ=255)
                                                              aTTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGa                                                                        <  2:412272/141‑1 (MQ=35)
                                                                ttCGTGGCATGGCGAANACCCGTAGATCTGAAGAGACCTGGGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACg                                                                      <  1:457208/141‑1 (MQ=255)
                                                                      gCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATc                                                                <  1:207163/141‑1 (MQ=39)
                                                                            cGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTc                                                          <  1:171079/141‑1 (MQ=39)
                                                                                 aTCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATAAATTCAAAACCGTTTAAAGTATGCTGTCCTGGACGGAGACTGTTTCGCCTTGTCTTTCTTACTTTAATATGGCGGTGAACTTGCTCAATGa                                                     >  2:584409/1‑141 (MQ=11)
                                                                                   ccttAGACCTGAAGAGACCTCACGTTCATTTTATAGAGAGCGTAAATACCTTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTACTATGACGGTGATCTTGCTCAATGAgg                                                   <  1:139639/138‑1 (MQ=11)
                                                                                         aTCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTc                                             >  2:92473/1‑141 (MQ=38)
                                                                                            tGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTACCTACATTTTATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGa                                          <  1:317754/141‑1 (MQ=255)
                                                                                            tGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGa                                          <  1:350650/141‑1 (MQ=39)
                                                                                             atattgaCCTGCGGTTCTTTTTATATAGAGCGTAAATACACTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGat                                         <  1:226796/136‑1 (MQ=255)
                                                                                              aaGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATCCCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGata                                        >  2:317204/1‑141 (MQ=37)
                                                                                                  gaCCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACTTTTTAAAGTATTCTTTGCTGTATTTATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGTTGATCTTGCTCAGTGAGGTTATTCAGATAtttt                                    >  1:358981/1‑140 (MQ=255)
                                                                                                   aCCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGATGGTATTCAGATATTTCg                                   <  2:371902/141‑1 (MQ=255)
                                                                                                            tCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAAt                          >  1:277316/1‑141 (MQ=38)
                                                                                                                   ttataGAGCGTAAATACATTCAATACCTTTTAAAGTATTTTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTc                   <  2:606110/140‑1 (MQ=255)
                                                                                                                   atataGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTc                   <  1:299872/141‑1 (MQ=255)
                                                                                                                     ataGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAg                 <  1:171427/141‑1 (MQ=255)
                                                                                                                       agagCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCCATAAGGTTCTTCAGATATTTCGCTGTACAATGACGTTCAgat               >  1:185831/1‑139 (MQ=14)
                                                                                                                       agagCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCCGTATTGATACTCTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGgt               >  1:541692/1‑141 (MQ=255)
                                                                                                                          gCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGgttta            <  2:277316/141‑1 (MQ=40)
                                                                                                                            gTAAATACATTCAATACCTTTTAAAGTATTCTTTTCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGgtttaag          <  1:200335/141‑1 (MQ=255)
                                                                                                                            gTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGgtttaag          <  1:334490/141‑1 (MQ=255)
                                                                                                                             tAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGgtttaagt         <  1:563098/141‑1 (MQ=255)
                                                                                                                               aaTACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACATTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGgtttaagttt       <  1:438594/141‑1 (MQ=255)
                                                                                                                                aTACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTTAATAAGGTTATTCATATATTTCGATGTACAATGACAGTCAGgttttagttta      >  1:39995/1‑141 (MQ=255)
                                                                                                                                aTACACTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGGCAGTCAGgtttaagttta      >  1:559015/1‑141 (MQ=255)
                                                                                                                                 tACATTCACTACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACATTGTCTTTCTTACTTTAATATGACGGTGATCTTGCGCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGgtttaagtttaa     >  2:450680/1‑141 (MQ=255)
                                                                                                                                    aTTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCACTGAGGTTATTCACATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAg  <  1:418808/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                           
AAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTATTCTTTGCTGTATTGATACTTTGATACCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAG  >  CP000730/35837‑36109

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: ‑