Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,440,085 G→T 100% intergenic (‑45/+126) cspA_2 ← / ← USA300TCH1516_01338 Cold shock protein CspA/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,440,0850GT99.6% 34.5 / ‑7.3 17intergenic (‑45/+126)cspA_2/USA300TCH1516_01338Cold shock protein CspA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base T (7/8);  total (7/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
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.

TACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATA  >  USA300TCH1516_ALE/1439957‑1440195
                                                                                                                                |                                                                                                              
tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaa                                                                                                    <  2:74134/141‑1 (MQ=255)
                 ctcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCTTAATCTGTAACCTCCAAGACTTAAATTCATTCAATATGCTTTTTCTCATATTACAAAAAATACATGCAAAGTTCa                                                                                   >  1:15414/1‑141 (MQ=255)
                   ccTTCCACTTCGATCAAGCCGAATCCTTTTTCATCGTTAATCCATTTAACTGTACCTGGTTTCATAATCTCAAACCTCCAAGACTAAATGTCATTCCATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACt                                                                                 <  2:194986/141‑1 (MQ=255)
                                   aGCCGAATCCTTTTTCAGCATTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCATTATGCTTATTCTCATATTTCAAAAAATACAGGCAAATTTCACTCAAAAATACttgtcaa                                                                 >  1:36245/1‑136 (MQ=255)
                                    gCCGAATCCTTTTTCTGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACCCATATATTCTTTGCAat                                                                >  1:294704/1‑141 (MQ=255)
                                          tCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACATCCAAGACTAAAATTCATTCAATATGCTTATTATCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTGGCATTATGGaa                                                          >  1:360477/1‑141 (MQ=255)
                                           ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat                                                         >  2:396006/1‑141 (MQ=255)
                                                   aGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCt                                                 >  1:181229/1‑141 (MQ=255)
                                                     cGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGc                                               <  1:102952/141‑1 (MQ=255)
                                                        tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATAAAAATAATAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTa                                            <  2:146991/141‑1 (MQ=255)
                                                                ttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat                                    <  1:183835/141‑1 (MQ=255)
                                                                ttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat                                    <  1:183787/141‑1 (MQ=255)
                                                                                           taCCCCCAATACTAAAATTCATTCCATCTGCTTATTCTAATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGCAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaa         <  1:380729/140‑1 (MQ=255)
                                                                                           aaCCTCCAAGACTAAAGTTCAATCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCTGGTATTACCAAATTGcaa         >  1:203339/1‑141 (MQ=255)
                                                                                              cTCCAAGACTAAATTTCATTCTATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatac      <  1:119120/141‑1 (MQ=255)
                                                                                              cTCAAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatac      <  2:274897/141‑1 (MQ=255)
                                                                                                  caGACAAACATACATGCAAGATGCGTATGCGTATATTACAAAAAATACATGCAAATCTCACTCAAAGATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaata  <  2:271618/140‑1 (MQ=255)
                                                                                                                                |                                                                                                              
TACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATA  >  USA300TCH1516_ALE/1439957‑1440195

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: ‑