Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,441,328	C→T	Q116Q (CAG→CAA)	rpsD ←	30S ribosomal subunit protein S4

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,441,328	0	C	T	100.0%	59.1 / NA	22	Q116Q (CAG→CAA)	rpsD	30S ribosomal subunit protein S4
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (12/10);  total (12/10)

AATGTCCGCAGACAGATCAGAACGCTCCGGCTTACGCTTAAACGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGCTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGACGTGCTGCTTCTTTGTAGTAGTTACGGAACTGACGCTCCAGCACACCATAGATACGGCGAACTTTTTGCTTTTCACGCAACT  >  NC_000913/3441091‑3441515                                                                                                                                                                                                                                              |                                                                                                                                                                                            aaTGTCCGCAGACAGATCAGAACTCTCCGGCTTACGCTTAAACATACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTGGCTTTTCACTCTGCTCAGCCAGCTCCAGAGCGTCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGGCTAACCTGGTAAGAAGTGATGTTATCATCACGACCGGTTGCCATAATTGCTTGATGGCTAACCAGTTGACGTGCTTcc                                                                                                                                                                                 <  1:238792/250‑2 (MQ=255)             cagaTCAGAACGCTCCGGCTTACGCTTAAACGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTCTgn                                                                                                                                                                               <  1:33875/240‑2 (MQ=255)               gaTCAGAACGCTCCGGCTTACGCTTAAACGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCAGTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCg                                                                                                                                                                  <  1:126706/251‑1 (MQ=255)                         cTCCGGCTTACGCTTAAACGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTc                                                                                                                                                                                  >  1:4976/1‑225 (MQ=255)                                 tACGCTTAAACGTACCTTCCATCTTGCCAGCAGCAACATCCAGCCAGGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATAc                                                                                                                                                 <  1:26133/250‑1 (MQ=255)                                          aCGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCGTTATTGCTAACCAGTTGACGTGCTTCTTCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTcc                                                                                                                                       <  1:214511/251‑1 (MQ=255)                                                             aGCATCAACTTCCAGCCAGGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCTCGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGACGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTATCCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGTTATACAACGTTGTCCAGACGACCTTCCAGCagag                                                                                                                    <  1:135040/251‑1 (MQ=255)                                                                              agGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAAGTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCGTCCAGCAGAGCCAACAGGTTTTCACCg                                                                                                   <  1:133409/251‑1 (MQ=255)                                                                                    ncTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGAGAGACTGATTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACTTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATACTTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGCGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTc                                                                                                       >  1:57340/2‑241 (MQ=255)                                                                                    ncTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCAAGCGAGACTGCTTCTTCGCTTTCTCAAGAATGCTTACACCGTCATTCGGCCTAACCTGATACGACGCGCTGTTAACAACACGACCGTTTACCATCATTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGtttt                                                                                                        >  1:37665/2‑240 (MQ=255)                                                                                              ctgctCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGATTACAACCTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGAc                                                                                   >  1:294179/1‑251 (MQ=255)                                                                                                 ntCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGcc                                                                                                                                                             >  1:81969/2‑174 (MQ=255)                                                                                                                             cgAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATACGAAGCGATGTTAACAACACGCCCGTTTACCATAATTGCTTTATGGCTAACCAGTTGCCGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGACGTGCTGCTTCTTTGTAGTAGTTACGGAACTg                                                    >  1:234187/1‑251 (MQ=255)                                                                                                                                    gCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGAACTAACCTGATGTTAAGCGATGTTCACAAAAAGACCGTTTACCATAATTGCTTTACGGCTCACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGAAGACGTTCCCGCAGAGCCAACAGGTTTTCACCGGTGATGCATTTCAGACGtgc                                                                               >  1:171544/1‑217 (MQ=255)                                                                                                                                                 ctcACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACCTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGACGTGCTGCTTCTTTGTAGTAGTTACGGAACTGACGCTCCAGCACACCAt                                   >  1:161928/1‑248 (MQ=255)                                                                                                                                                           cgtACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGACGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGACGTGCTGCTTCTTTGTAGTAGTTACGGAACTGACGCTCCAGCACACCATAGATACGGCGAAc                      >  1:310661/3‑251 (MQ=255)                                                                                                                                                             tACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGAAAGTTTACCATAATTGCCTTATGGATAACCAGTTGACGTGCCTCTGCAAGCGTGGCACCGAACCCCATACGGAATACACCGCTGTCCAGAAGACCTCACACCAGAGCCAACAGCCTTTCACCGGTGATGCCTTTCAGa                                                                                    >  1:285378/1‑187 (MQ=255)                                                                                                                                                                         cGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACTGGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATGCTATGTTGTCCAGACGACCTTCCAGCAGAGGCAACAGGTTTTCGCCGGTGTGGTCTTGCGGATGTGCGGCCTCTTTGTATTAGGTACTGAACTGACGCTCCAGCACACCAGAGATACGGCGAACTTTTTGCTTTTCa         <  1:289364/250‑1 (MQ=255)                                                                                                                                                                           gACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAAGTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGGTGTCCAGACGACCGTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGACGTTCTGCTTCTTTgtagt                                                                 <  1:130815/192‑1 (MQ=255)                                                                                                                                                                               aaCCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGACGTGCTGCTTCTTTGTAGTAGTTACGGAACTGACGCTCCAGCACACCATAGATACGGCGAACTTTTTGCTTTTCACGCAACt  >  1:10934/1‑251 (MQ=255)                                                                                                                                                                               aaCCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGACGTGCTGCTTCTTTGTAGTAGTTACGGAACTGACGCTCCAGCACACCATAGATACGGCGAACTTTTTGCGTTTCACGCAAc   <  1:256760/250‑1 (MQ=255)                                                                                                                                                                                                                          aTTGCTTTATGGCTAACCAGTTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCANNAGAGCCNNc                                                                                                               >  2:14710/1‑99 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                            AATGTCCGCAGACAGATCAGAACGCTCCGGCTTACGCTTAAACGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTGGCTTTTCACGCTGCTCAGCCAGCTCCAGAGCGGCTTTCACGCGAGACTGCTTCTTCGCTTTCTCACGAATGCTTACAACGTCATTCGGACTAACCTGATAAGAAGCGATGTTAACAACACGACCGTTTACCATAATTGCTTTATGGCTAACCAGCTGACGTGCTTCTGCACGAGTGGCACCGAAGCCCATACGGTATACAACGTTGTCCAGACGACCTTCCAGCAGAGCCAACAGGTTTTCACCGGTGTTGCCTTTCAGACGTGCTGCTTCTTTGTAGTAGTTACGGAACTGACGCTCCAGCACACCATAGATACGGCGAACTTTTTGCTTTTCACGCAACT  >  NC_000913/3441091‑3441515

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑