Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,440,085	G→T	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_ALE	1,440,085	0	G	T	96.4%	90.6 / NA	29	intergenic (‑45/+126)	cspA_2/USA300TCH1516_01338	Cold shock protein CspA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (11/16);  minor base C (1/0);  total (12/17)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTAG  >  USA300TCH1516_ALE/1439940‑1440228                                                                                                                                                  |                                                                                                                                                ttAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCa                                                                                                                                               >  4:216611/1‑148 (MQ=255)      tGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAACTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTa                                                                                                                                          >  4:6862/1‑148 (MQ=255)          gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa                                                                                                                                      >  3:89538/1‑148 (MQ=255)             aaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaaa                                                                                                                                   <  4:62511/148‑1 (MQ=255)                 gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa                                                                                                                                      >  1:20205/1‑141 (MQ=255)                   aCGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATg                                                                                                                             <  3:175702/148‑1 (MQ=255)                          cGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCCTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAttt                                                                                                                      <  4:209095/148‑1 (MQ=255)                            tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCa                                                                                                                    <  4:301789/148‑1 (MQ=255)                             cATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc                                                                                                                   >  3:34671/1‑148 (MQ=255)                             cATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGAACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCCCATATTACAAAAAATACATGCAAATTTCAc                                                                                                                   >  3:211701/1‑148 (MQ=255)                                               cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                        <  1:34209/141‑1 (MQ=255)                                                 aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCACGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                                               <  4:305585/148‑1 (MQ=255)                                                 aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGAATAAAATTCATTCAATATGCTTATAAAAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                                               <  4:146575/148‑1 (MQ=255)                                                  tAAAGCCGAATCCTTTTTCCGCGTACGGCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg                                                                                                     <  2:65787/141‑1 (MQ=255)                                                                ttttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataat                                                                                       <  2:59778/141‑1 (MQ=255)                                                                    cAGCGTTAAACCATTTAACTGTACCATATTTCATAATCTGAAACCTCCAAGACTAAAATTCATGCAATATGCTTATTATAATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTaa                                                                            <  4:113389/148‑1 (MQ=255)                                                                       cGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACtt                                                                         >  4:10042/1‑148 (MQ=255)                                                                         ttAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                                                                       >  4:357101/1‑148 (MQ=255)                                                                                aTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAg                                                                >  3:170754/1‑148 (MQ=255)                                                                                 tttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGta                                                                      <  1:42306/141‑1 (MQ=255)                                                                                         tACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttat                                                       <  3:216611/148‑1 (MQ=255)                                                                                              tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa                                                  >  3:42183/1‑148 (MQ=255)                                                                                              tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTGATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa                                                  >  3:11469/1‑148 (MQ=255)                                                                                                  tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                                              <  3:121695/148‑1 (MQ=255)                                                                                                       aTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGTAGTTATTACCAAATTGcaat                                         <  3:179491/148‑1 (MQ=255)                                                                                                       aTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaat                                         <  3:370350/148‑1 (MQ=255)                                                                                                            aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaat                                    >  4:147577/1‑148 (MQ=255)                                                                                                                                cattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa                <  4:15915/148‑1 (MQ=255)                                                                                                                                              aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTAg  <  3:313149/148‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                TTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTAG  >  USA300TCH1516_ALE/1439940‑1440228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑