Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,356,088	C→T	13.3%	M353I (ATG→ATA)	yclM ←	Aspartokinase 3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,356,088	0	C	T	13.3%	73.0 / 5.4	30	M353I (ATG→ATA)	yclM	Aspartokinase 3
Reads supporting (aligned to +/- strand):  ref base C (8/18);  new base T (2/2);  total (10/20)
Fisher's exact test for biased strand distribution p-value = 5.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.34e-01

GACTTTATTCATACCTTCGCCGACAATCATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTAAAGCCGACTTGTCTATTCATTAAATACTTTTTGATATTAATAACGGTAAAATC  >  USA300TCH1516_ALE/1355956‑1356228                                                                                                                                     |                                                                                                                                             gACTTTATTCATACCTTCGCCGACAATCATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGAt                                                                                                                                      >  1:256195/1‑141 (MQ=255)             aCCTTCGCCGACAATCATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATc                                                                                                                          >  1:287201/1‑141 (MQ=255)               cTTCGCCGACAATCATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGATTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCaa                                                                                                                        <  2:293689/141‑1 (MQ=255)                 ccGCCGACAATCATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATa                                                                                                                      <  2:295895/140‑1 (MQ=255)                    ccGACAATCATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCt                                                                                                                   >  1:321723/1‑141 (MQ=255)                            cATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGTATAACGATACTGATAGTATCAATACCTGAAGGCat                                                                                                           >  1:145382/1‑141 (MQ=255)                            cATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGTATAACGATACTGATAGTATCAATACCTGAAGGCat                                                                                                           >  1:145390/1‑141 (MQ=255)                               tAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATATCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATGCTGATAGTATGAATACCTGAAGGCATATg                                                                                                        >  2:182661/1‑141 (MQ=255)                                  tatTGCTAAATCATGCTCCATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACTCATAACGTTACTGCTAGTATCAATACCTGAAGGCATATGATc                                                                                                     <  1:94978/141‑1 (MQ=255)                                  tatTGCTAAATCATGCTCAATAGTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAAAACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGCCACTTTTAGTAGCAATACCTGAAGGCATATGATc                                                                                                     <  1:94970/141‑1 (MQ=255)                                  tatTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATc                                                                                                     <  1:133726/141‑1 (MQ=255)                                    ttGGTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCaa                                                                                                   <  2:116447/141‑1 (MQ=255)                                     tGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCaaa                                                                                                  >  1:144549/1‑141 (MQ=255)                                              ctGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAAtatt                                                                                         <  1:241326/140‑1 (MQ=255)                                              ctGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAAtatt                                                                                         <  1:234433/140‑1 (MQ=255)                                                 cTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAAtattatt                                                                                      >  2:92417/1‑141 (MQ=255)                                                       aCTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCctc                                                                                <  1:379455/141‑1 (MQ=255)                                                        cTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCctct                                                                               <  2:377024/141‑1 (MQ=255)                                                                 tcaACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCt                                                                      <  1:284348/141‑1 (MQ=255)                                                                     cATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATGCCTGTAGGCATATGATCAAATGAATTATTATTATCCTCTAAGACACCTAata                                                                  >  2:161756/1‑141 (MQ=255)                                                                               ttGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGt                                                        <  2:259095/141‑1 (MQ=255)                                                                                 gACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGTATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTaa                                                      <  2:145382/141‑1 (MQ=255)                                                                                 gACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGTATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTaa                                                      <  2:145390/141‑1 (MQ=255)                                                                                   cGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTAAAg                                                    <  1:179188/141‑1 (MQ=255)                                                                                            tttAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTAAAGCCGACTTGt                                           <  2:95905/141‑1 (MQ=255)                                                                                            tttAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTAAAGCCGACTTGt                                           <  2:327874/141‑1 (MQ=255)                                                                                                       tGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTTAGACACCTAATATCTTTCTAGTAAAGCCGACTTGTCTATTCATTaa                                <  2:6705/141‑1 (MQ=255)                                                                                                         tttCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTACGACACCTAATATCTTTCTAGTAAAGCCGACTTGTCTATTCATTAAAt                              <  2:256195/141‑1 (MQ=255)                                                                                                                      aaTTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTAAAGCCGACTTGTCTATTCATTAAATACTTTTTGATAtt                 >  1:72027/1‑141 (MQ=255)                                                                                                                                 aaCGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTAAAGCCGACTTGTCTATTCATTAAATACTTTTTGATATTAATAACGGTaa      <  2:229881/141‑1 (MQ=255)                                                                                                                                     cATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAGTGAAATATTCTTATCCTCTAAGACACCTAATATCTTTCTAGTAAAGCCGACTTGTCTATTCATTAAATACTTTTTGATATTAATAACGGTAAAATc  >  2:142715/1‑141 (MQ=255)                                                                                                                                     |                                                                                                                                             GACTTTATTCATACCTTCGCCGACAATCATTAATATTGCTAAATCATGCTCAATACTTAGCTCATCAACATCACATTTTTGACGAATTTCATTTAATACTTTTGTTTCTTTATTTTGAATTTGTTTTGAACGCATAACGATACTGATAGTATCAATACCTGAAGGCATATGATCAAATGAAATATTATTATCCTCTAAGACACCTAATATCTTTCTAGTAAAGCCGACTTGTCTATTCATTAAATACTTTTTGATATTAATAACGGTAAAATC  >  USA300TCH1516_ALE/1355956‑1356228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑