Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 517,732 T→C 17.1% intergenic (+5800/‑963) recR → / → speA_2 Recombination protein RecR/Arginine decarboxylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE517,7320TC17.1% 47.6 / 4.6 32intergenic (+5800/‑963)recR/speA_2Recombination protein RecR/Arginine decarboxylase
Reads supporting (aligned to +/- strand):  ref base T (18/8);  new base C (3/3);  total (21/11)
Fisher's exact test for biased strand distribution p-value = 3.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATGTCTAAAA  >  USA300TCH1516_ALE/517598‑517872
                                                                                                                                      |                                                                                                                                            
gAATACTAATCGATCGAAAACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTAGTAACTATAGCAAGAAGGTCACACCCGTTTCCATGc                                                                                                                                        >  2:30096/1‑141 (MQ=11)
  aTACTAATCGATCGAACACTTAATCAAAATAGATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCg                                                                                                                                      <  1:291427/141‑1 (MQ=17)
     cTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAac                                                                                                                                   <  1:238044/141‑1 (MQ=32)
             tagaAGATTTAATCAAAATAAATGTTTTGCGAAGCAATATCAATTTTACTTACTATCTAGTTTTGAAGGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGt                                                                                                                           <  2:36194/139‑1 (MQ=255)
                 aGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGGCACACCTGTTTCCATGCCGAAAACAGAAGTTAAg                                                                                                                       >  1:249663/1‑141 (MQ=17)
                 aGACTTAATCAAAATAAATGTTTTGCGAAGCAAAAGCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAAGTCACACCTGTTTCCATGACGAACACAGAAGGTAAg                                                                                                                       >  2:91148/1‑141 (MQ=255)
                   aCTTAATCAATATTAATGTTTTGCGGAGCAAAAGCACTTTTACTTACTATCTAGTTTTGAATGGATAAATTACATTCATATGTCTGGTGACTATAGCAAGTAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCt                                                                                                                     <  2:44606/141‑1 (MQ=11)
                    cTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTc                                                                                                                    >  2:257502/1‑141 (MQ=32)
                             aataaatGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTc                                                                                                           >  1:125092/1‑141 (MQ=32)
                                  atGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTCGCGTCGATgg                                                                                                      >  2:185521/1‑141 (MQ=17)
                                       ttGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTGCTTAGCGTCGATGGTAGTc                                                                                                 >  1:174212/1‑141 (MQ=17)
                                              gCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCTTAATACATAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTa                                                                                          >  1:211788/1‑141 (MQ=255)
                                                    tCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGCAGTTAAGCTACTTAGCGCCGATGGTAGTCGAACTTACGTTcc                                                                                    >  1:117187/1‑141 (MQ=12)
                                                        ttttACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTa                                                                                <  1:222969/141‑1 (MQ=32)
                                                                         ttttGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGGGTAGAAGGTTGCCAg                                                               >  1:159378/1‑141 (MQ=17)
                                                                         ttttGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAg                                                               <  1:257502/141‑1 (MQ=32)
                                                                             gAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCaa                                                           >  1:166984/1‑141 (MQ=32)
                                                                                      aaTTAGCTTCATATGTCTTGGTACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaat                                                  >  2:222683‑M2/1‑131 (MQ=255)
                                                                                            aTTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGGAACAAATGGAGGCGGTg                                            >  2:244110/1‑141 (MQ=255)
                                                                                                    ggttagTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCAGAACACAGAAGTTAAGTTCCTTAGCGTCGAGGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCAt                                    <  1:129996/136‑1 (MQ=255)
                                                                                                       tGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTga                                 >  1:70227/1‑141 (MQ=32)
                                                                                                         gTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTgcga                               >  1:8052/1‑141 (MQ=17)
                                                                                                            aCTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTCCGTTCCGCTAGAGTCGAACGTTGCCAGGCAgtttcttaatcaaattttgggtaaaaaatcaa                            <  2:175715‑M2/141‑33 (MQ=255)
                                                                                                             cTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTACATGCCTTCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGc                           >  1:292881/1‑141 (MQ=11)
                                                                                                                     aggaggTCACACATGTTCCAATGACGAAGACAGAAGTTAAGCTCCTTAGCGTCGAGGGTAGTCGAAATTACGATCCGCTAGAGTAGAACGTTGACAGGCAgttttataatcaaattttggttaaaaaataaaatggacaag                   >  2:264798‑M2/1‑100 (MQ=255)
                                                                                                                         ggTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGAAGTCGAACTTACGTTCCGCTAGAGAAGAACGTTGCAAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCACAAGGTCTCtttt               >  1:32899/1‑141 (MQ=255)
                                                                                                                          gTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCCAGAGCAGCACGTTGCCAGGCAgtttcttaatcaaattttggttaaaaactaaactggccaagctagc              <  2:262919‑M2/141‑47 (MQ=255)
                                                                                                                          gTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGCAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGGCACGTAgttttgtaagcaaactttgcttgaaaactaaaaaagacaagataaa              <  2:267922‑M2/141‑47 (MQ=255)
                                                                                                                           tCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaataaaatggacaagataaaa             >  1:255208‑M2/1‑94 (MQ=255)
                                                                                                                           tCAAACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGAATGGGATGACACGCATTGAGAAAGAAAGATCTCattttt             >  2:63403/1‑141 (MQ=11)
                                                                                                                               acCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTCGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTCTg         >  1:92001/1‑141 (MQ=17)
                                                                                                                                ccTGGTTCCATGCCGAACACAGAAGTTAAGCGCCTGAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCTAGGTCTCTTTTTTTATGt        <  2:211788/141‑1 (MQ=255)
                                                                                                                                      tCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATGTCTaaaa  >  1:289236/1‑141 (MQ=33)
                                                                                                                                      |                                                                                                                                            
GAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATGTCTAAAA  >  USA300TCH1516_ALE/517598‑517872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: