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	100.0%	53.6 / NA	19	S623S (TCA→TCC)	gspD	Type II secretion system protein GspD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (7/12);  total (7/12)

GCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGAC  >  NC_000913/3458013‑3458490                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                      ncGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCg                                                                                                                                                                                                                                     >  1:133114/2‑251 (MQ=255)                                                                              ntctTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCatat                                                                                                                                                        >  1:281657/2‑251 (MQ=255)                                                                                        ataCCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACCCCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGGGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATtcac                                                                                                                                              <  1:444946/251‑1 (MQ=255)                                                                                          aCCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTGGATCGCTTACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAgc                                                                                                                                                                                                                                                  <  1:446315/149‑1 (MQ=255)                                                                                                     gcgcgcTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGcc                                                                                                                                                                                        >  1:29703/1‑196 (MQ=255)                                                                                                      cgcgcTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGACATTCATATGAGAATTCACTCACCGTACCCCgn                                                                                                                                <  1:110197/251‑2 (MQ=255)                                                                                                                                  tccgtccgACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCTTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACCCGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTgn                                                                                                     <  1:268678/250‑2 (MQ=255)                                                                                                                                                  ccGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTGACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAgg                                                                                    <  1:231133/251‑1 (MQ=255)                                                                                                                                                    gTGACGATGAGGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGGTACCGTCAGGAGCAACAACAGCGGATCGACGTGAAATCCAAAGCGCTGGTTGGc                                                                                                                                                                                                                                        <  1:152040/101‑1 (MQ=255)                                                                                                                                                                                      aaaaTACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCAGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCCCCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGc                                                <  1:185145/250‑1 (MQ=255)                                                                                                                                                                                                       gTCAGGAGCAACATCAGCGGATCGACGGAAAATCCAAAGCGCTGGTTGTCTCTGAAGATTTTCCGGTGCTTGATGAAAGCGCTTCCAACGTTCACGCCCCTGCGCCAGCGTCACGGTCAGGGATTCATATGATGTTTTTCTCACCGTACCCCGCCAGTTGGGCGGTGGCACAACGAATTGGTTAtctc                                                                                              <  1:398489/188‑1 (MQ=255)                                                                                                                                                                                                           ggAGCNGCAACNGNNGATCGACGGGAAATCCAAANCGCTGGTTGGCTCGGNAGATNTGCCgntgntn                                                                                                                                                                                                                   >  2:180479/1‑66 (MQ=255)                                                                                                                                                                                                               caacaaCAGCGGAGCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGt                       <  1:180479/251‑1 (MQ=255)                                                                                                                                                                                                                        ctgATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTg              >  1:427871/3‑251 (MQ=255)                                                                                                                                                                                                                        cGGATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGAGCTGGATGAAAACACGTTCAACAGTCAAGCCCCTGCGCCATCGTAACGGTGAGGCATTCATCTgag                                                                                                                                                     >  1:165794/1‑116 (MQ=255)                                                                                                                                                                                                                         ggATCGACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAACCACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTgn             <  1:90395/251‑2 (MQ=255)                                                                                                                                                                                                                          nnnnnnnnnnaanNNNNAAGNGCTGGTTGGTTCGGAAGATTTGCCGGTGCTGGATGAAAACACTTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACaa                                                                                                             <  2:281657/144‑1 (MQ=255)                                                                                                                                                                                                                              gACGGGAAATCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCTGCCAGTTGGGCGCTGGCACATCGAATTGGTGATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGGTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGAc        <  1:332604/251‑1 (MQ=255)                                                                                                                                                                                                                                    aaaTCCAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACCCGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGAGACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGAc  <  1:305698/251‑1 (MQ=255)                                                                                                                                                                                                                                     aaTCCAAAGCGCTGGTTGGCTCGGAAGATTTGACGGTGCTGGATGAAAACACGTGCAAAAGGCACGCCCCTGCGCCATAGTCAAGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTAGAGCGGTTACTCGATATTCAACGTCAGGtagtcagctgacgctgagcatt  >  1:397074/1‑229 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                      GCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACCGTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGAC  >  NC_000913/3458013‑3458490

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑