Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,790,9820AG22.9% 55.1 / 17.8 35I446M (ATA→ATG) manPPTS system mannose‑specific EIIBCA component
Reads supporting (aligned to +/- strand):  ref base A (10/17);  new base G (4/4);  total (14/21)
Fisher's exact test for biased strand distribution p-value = 6.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.63e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AACATCATTGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACATGATACAGAGGTTGACAATG  >  USA300TCH1516_ALE/2790848‑2791118
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aaCATCATTGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAgtaggt                                                                                                                                    <  1:114427/141‑1 (MQ=255)
    tcatTGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATGGTAGGTAGTc                                                                                                                                >  1:4531/1‑141 (MQ=255)
    tcatTGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATGGTAGGTAGTc                                                                                                                                >  1:5675/1‑141 (MQ=255)
    tcatTGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATGGTAGGTAGTc                                                                                                                                >  1:192913/1‑141 (MQ=255)
    tcatTGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATGGTAGGTAGTc                                                                                                                                >  1:134085/1‑141 (MQ=255)
    tcatTGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTc                                                                                                                                >  2:140560/1‑141 (MQ=255)
       ttGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTGATCTTTGCAGTGATAGTAGGTAGTCTTg                                                                                                                             <  2:77167/141‑1 (MQ=255)
           tGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTcac                                                                                                                         <  2:21769/141‑1 (MQ=255)
               aTGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATg                                                                                                                     <  1:161416/141‑1 (MQ=255)
                tGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGa                                                                                                                    <  1:130000/141‑1 (MQ=255)
                  aTTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGact                                                                                                                  >  1:78163/1‑141 (MQ=255)
                   ttGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGacta                                                                                                                 >  2:16334/1‑141 (MQ=255)
                   ttGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATAGTATATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGacta                                                                                                                 >  1:171497/1‑141 (MQ=255)
                          aGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACt                                                                                                          >  1:207583/1‑141 (MQ=255)
                             cATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACtatt                                                                                                       <  1:52356/141‑1 (MQ=255)
                                       aTTTGTGGTGACGGCGATAGACTCGCACATTGAGGTCCATTCGTGGCTGGATTGGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGCCTTGTCACAAAGACTACTGTACTATTATTAAAACGc                                                                                             <  2:220523/141‑1 (MQ=255)
                                       aTTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGc                                                                                             <  1:136779/141‑1 (MQ=255)
                                               tgtCGGCGATAGGGTCGCACATGGAGGTGCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTTATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACAcc                                                                                     <  2:157777/141‑1 (MQ=255)
                                                                      gAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAg                                                              <  2:207583/141‑1 (MQ=255)
                                                                                cGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAacacac                                                    >  2:173625/1‑141 (MQ=255)
                                                                                              gtggtATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATa                                      >  2:103113/1‑141 (MQ=255)
                                                                                               tggtATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATAc                                     >  1:182409/1‑141 (MQ=255)
                                                                                                 gtATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCGGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAg                                   <  2:193576/141‑1 (MQ=255)
                                                                                                             tattatGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACacaac                       <  1:127466/141‑1 (MQ=255)
                                                                                                              tttatGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACacaaca                      <  2:171497/140‑1 (MQ=255)
                                                                                                              attatGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACacaaca                      <  1:16334/141‑1 (MQ=255)
                                                                                                               ttatGGTTTATCTTTGCAGTGATGGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACAt                     <  2:192913/141‑1 (MQ=255)
                                                                                                               ttatGGTTTATCTTTGCAGTGATGGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACAt                     <  2:134085/141‑1 (MQ=255)
                                                                                                               ttatGGTTTATCTTTGCAGTGATGGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACAt                     <  2:4531/141‑1 (MQ=255)
                                                                                                               ttatGGTTTATCTTTGCAGTGATGGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACAt                     <  2:5675/141‑1 (MQ=255)
                                                                                                                          cTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACATGATACAGAGGt          <  2:197911/141‑1 (MQ=255)
                                                                                                                          cTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACATGATACAGAGGt          <  1:140560/141‑1 (MQ=255)
                                                                                                                             tGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACATGATACAGAGGTTGa       >  2:212783/1‑141 (MQ=255)
                                                                                                                                 gTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACATGATACAGAGGTTGACAAt   >  2:114357/1‑141 (MQ=255)
                                                                                                                                  tGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACATGATACAGAGGTTGACAATg  <  2:68865/141‑1 (MQ=255)
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AACATCATTGGTGCAATGATTGCATCAGTCATTGCAGCCATTGGTGGTGTCGGCGATAGAGTCGCACATGGAGGTCCAATCGTGGCTGTATTAGGTGGTATTGATCATGTATTATGGTTTATCTTTGCAGTGATAGTAGGTAGTCTTGTCACAATGACTACTGTACTATTATTAAAACGCAATACACCAGTTATAGCAGTAGATGCACCAGCGCAACACACGCAACTTCATGATACAGATATTACACAACATGATACAGAGGTTGACAATG  >  USA300TCH1516_ALE/2790848‑2791118

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