Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,352,815 G→A 100% A92V (GCA→GTA)  rpsI ← 30S ribosomal protein S9

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,352,8150GA100.0% 100.5 / ‑6.5 33A92V (GCA→GTA) rpsI30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (18/14);  minor base C (1/0);  total (19/14)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAAT  >  USA300TCH1516_ALE/2352678‑2352951
                                                                                                                                         |                                                                                                                                        
tatCGTCCGACAATTAACGTTTTGAGAAATGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACtt                                                                                                                                       <  1:566227/141‑1 (MQ=255)
taccGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGATGCATTACGTCCTGGTTTATTCCCTTCTTTCTTACGTAGTTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACtt                                                                                                                                       <  1:639231/138‑1 (MQ=25)
     tCCTACAATTATCGTTTTGAGAATTGAGGTGATCGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaat                                                                                                                                  <  1:546754/141‑1 (MQ=255)
       cGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaataa                                                                                                                                <  1:179185/141‑1 (MQ=255)
          cAATTAACGTTTTGTGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTGTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGc                                                                                                                             >  1:437999/1‑141 (MQ=255)
          cAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATCCGTCGGCGTCGGGGGAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTATTAATGc                                                                                                                             >  1:189143/1‑141 (MQ=25)
          cAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTCCTTCTAATAATGc                                                                                                                             >  1:206757/1‑141 (MQ=255)
          cAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGc                                                                                                                             >  1:464734/1‑141 (MQ=255)
             ttAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACg                                                                                                                          <  1:350156/141‑1 (MQ=255)
                      tGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGCTCTACTTCTGATAATGCACGGGCGATTcc                                                                                                                 >  1:277539/1‑141 (MQ=255)
                             tGAGGTGAACGACCAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTAACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCGCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACgg                                                                                                          <  1:260025/141‑1 (MQ=255)
                                ggTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGCCGGATa                                                                                                       >  1:190944/1‑141 (MQ=255)
                                ggTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGAtg                                                                                                       >  1:570435/1‑140 (MQ=255)
                                      cgacgaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttga                                                                                                 <  1:474124/141‑1 (MQ=255)
                                                     aGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGaaa                                                                                  >  1:779954/1‑141 (MQ=255)
                                                            gTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAtccaccac                                                                           <  1:511246/141‑1 (MQ=255)
                                                                     gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGt                                                                  <  1:225012/141‑1 (MQ=255)
                                                                     gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTACAGTGAAACCACCACCATGAACGt                                                                  >  1:306439/1‑141 (MQ=255)
                                                                     gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCGTGTCCAGTGAAACCACCACGATGACCGt                                                                  >  1:660538/1‑141 (MQ=255)
                                                                        ttttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTaa                                                               <  1:6714/140‑1 (MQ=255)
                                                                            cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCCCCATGAACGTTAACTaa                                                           >  1:442677/1‑141 (MQ=255)
                                                                                      tCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAg                                                 >  1:508151/1‑141 (MQ=255)
                                                                                       cACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGt                                                <  1:457611/141‑1 (MQ=255)
                                                                                       cACGAGTAAGTAACACAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGt                                                <  1:306048/141‑1 (MQ=255)
                                                                                          gAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTAc                                             <  1:675733/141‑1 (MQ=255)
                                                                                               agtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTa                                        >  1:242028/1‑141 (MQ=255)
                                                                                                   aTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGACACCACCACCCTGAACGTTAACTAAAACATCATAGTTACCTTTAGttt                                    >  1:3904/1‑141 (MQ=255)
                                                                                                   aTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGttt                                    >  1:622057/1‑141 (MQ=255)
                                                                                                        gcgcGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGCGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAACCCACCACCATGAACGTTAACTAAAACCTCATAGTTACCTTTAGGTTCAGtt                               >  1:289273/1‑141 (MQ=255)
                                                                                                             ttttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCAACATGAACGTTAAGTAAAAAATAATAGTTACCTTTAGTTTCAGTTACAta                          >  1:640836/1‑140 (MQ=255)
                                                                                                                tAAACAACCTCTCTATTCAGGATCTACTTCTAATAACGCACAAGCGATTCCGTGATGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACAGCATAGTTACCTTTAGTTTCAGTTACATCaaa                       <  1:71788/141‑1 (MQ=255)
                                                                                                                          ctGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGttt             >  1:799590/1‑141 (MQ=255)
                                                                                                                                     aTCTACTTCTAATAATGCACGAGCGCTTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTCGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAAt  >  1:448086/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                        
TATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAAT  >  USA300TCH1516_ALE/2352678‑2352951

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: ‑