Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,458,245	A→C	S623S (TCA→TCC)	gspD →	Type II secretion system protein GspD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,458,245	0	A	C	89.3%	68.6 / 1.6	28	S623S (TCA→TCC)	gspD	Type II secretion system protein GspD
Reads supporting (aligned to +/- strand):  ref base A (2/1);  new base C (14/11);  total (16/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.78e-01

CCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCA  >  NC_000913/3458008‑3458492                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                        ccTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGtt                                                                                                                                                                                                                                             <  1:176122/250‑1 (MQ=255)   tGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGc                                                                                                                                                                                                                                          >  2:124085/1‑251 (MQ=255)    gggCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGc                                                                                                                                                                                                                                          <  1:200473/250‑1 (MQ=255)        ggATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGATGGTTGGCTCgg                                                                                                                                                                                                                                      >  1:321186/1‑250 (MQ=255)                     atTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTg                                                                                                                                                                                                                        <  1:103908/251‑1 (MQ=255)                             aaaGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCAGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGCTTTGCCGGTGCTGGAtc                                                                                                                                                                                                                 >  2:22633/1‑249 (MQ=255)                                   aaagtgaaaaaGGTTACTCTTCTGGGCGATAGTCCTTTAGGGGGGCAACTCCTCCGGTATACCTCCACCGAGCGCGCTAAACGCCACCTGATGGTATTTATCCGACCGCCTAGTATTCTTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACATCAGCGGATCTACGGGAAAACCAAATCACTTGTTGGCTTGGAAGATTTTCGGGTGCTGTATGAAAtcac                                                                                                                                                                                                          <  2:233967/243‑1 (MQ=255)                                                       gCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTg                                                                                                                                                                                      >  1:211284/1‑251 (MQ=255)                                                                              gtcAACTATTCCGCTATACATCCACCGAGCGCGCTAAACGCAACATGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGAAGGGAAATCCAAAGGGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGGTGAAAACACGTACAACAGTCCCGACCCTGCGCAATCGTGACgggggagcatt                                                                                                                                                               >  2:888/3‑242 (MQ=255)                                                                                cAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACATGCTGGTATTTATCCGTCCGACGATTATCCGGGACGATGATGTTTATCGCTCACTGTCAAAAGCGAAATACAACCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGTTGGTTGGCCCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTACACAGTCACGCCCCTGAGCCATAGTCCCGGTGAGGCATTct                                                                                                                                                             >  2:45917/1‑250 (MQ=255)                                                                                        ccGCTATACCTCCACCGAGCGCGCGAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAAGACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATgaga                                                                                                                                                      <  1:45917/250‑1 (MQ=255)                                                                                        ccGCTATACCTCCACCGAGCACGCTAAACGCAACCTGATGGTCTTTATCCGTCCGACGATTCTCCGTGACGATGATGTTTATCGCTCACTGTCAAACGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGCTCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTTCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCATCACGGAGAGGCATTCATATgaga                                                                                                                                                      >  2:162434/1‑250 (MQ=255)                                                                                             ataCCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATtcac                                                                                                                                                >  1:324890/1‑251 (MQ=255)                                                                                                  cccACCGAGCCCGCTAAACGCAACCTGATGTTATTTATCCGTCCGACGATTAGCCGTTACGATGATGTTTATCGCGCACTGTCAAAAGAGAAATACACCCGTTTCCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTGGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACTGTGAGGCATTCATATGAGAATTCACTCAcc                                                                                                                                           <  2:211284/250‑1 (MQ=255)                                                                                                            gcgcTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGaa                                                                                                                                                     <  1:339169/231‑1 (MQ=255)                                                                                                            gcgcTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGaa                                                                                                                                                     >  2:339169/1‑231 (MQ=255)                                                                                                                 aaaCGCAACCTGATGGTATGTATCCGTCCGACGATTATCCGTGCCTATGCTGTTTATCGCTCACTGTCAAAAGAGTAATACACCCGTTACCGTCAGGAGCATCAACCGCGGATCGACGGGAAATCCAAAGCGCTGGATGGCTCGGAAGATTTGCCGGTGCTTGATGAAAACCCGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTACGACCTTCATATGCGAATTCACTCACCGTACCCCGCCAGTTg                                                                                                                            >  2:170095/1‑251 (MQ=255)                                                                                                                         ccTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTgg                                                                                                                    >  1:88049/1‑251 (MQ=255)                                                                                                                         ccTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTgg                                                                                                                    <  1:124085/251‑1 (MQ=255)                                                                                                                                          gtccgACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAAtt                                                                                                                                                   <  1:115515/203‑1 (MQ=255)                                                                                                                                          gtccgACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAAAACGTTCCACAGTCACGCCCCTGCGCCATCGTCACGGGGCGGCATTCATATGAGAAtt                                                                                                                                                   >  2:115515/1‑203 (MQ=255)                                                                                                                                                           gACGATTATGTTTATCTCTCACTGTCAAAAGAGAAATACACCCGTTACCTTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTTGTTGGCTCGAAAGATTTGCCGGTGCTGGATTAAAACACTTTCAACAGCCACGCCCCTGCACCATCGTCTCGGTGAGGCATGCATATGAGAATTCACTCCCCTTCCCCCTCCAGTTGGGCGCTGTCACAACGAATTGTTTATCTCTATTCAGAGGGCga                                                                                  <  1:89012/251‑1 (MQ=255)                                                                                                                                                                                        agagAAATACACCCGTTACCGTCAGAAGCAAAAACAGCGAAACGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCAATCACCGTACCCCGACAGTTGGGCGCTGGCACAACGAATTGGTTATCTATCTTCAGAGGGCGAGATTATTTCTCTCGCCGATACGCCATTCg                                                     >  1:122837/1‑251 (MQ=255)                                                                                                                                                                                                      gTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGATCGGAAGATTTGCCGGTGCTGGATGAACACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTAAGGCATTCATATGAGCATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGATATCTCTATTCAGAGTGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGat                                       >  2:80949/1‑251 (MQ=255)                                                                                                                                                                                                               aGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGt                              >  1:78504/1‑251 (MQ=255)                                                                                                                                                                                                                    caacaaCAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGt                         >  1:59950/1‑251 (MQ=255)                                                                                                                                                                                                                             cGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATGTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTg                <  1:163393/251‑1 (MQ=255)                                                                                                                                                                                                                                           aTCAAAAGCTCTGGTTGGCTCGGAAGATTTACCGGTTCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCAGTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCa  <  1:162434/251‑1 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                        CCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCA  >  NC_000913/3458008‑3458492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑