Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,169,836	A→G	L180P (CTG→CCG)	ldtC ←	L,D‑transpeptidase LdtC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,169,836	0	A	G	96.2%	75.4 / ‑3.7	26	L180P (CTG→CCG)	ldtC	L,D‑transpeptidase LdtC
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (8/17);  total (9/17)
Fisher's exact test for biased strand distribution p-value = 3.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-01

GGCTGATGTACTTCAACCAGACGCGCACCGTTTGGTTCGGCAGAGACTTTTATCGGAGTGTTGATGATATTCACTTTGGTGCCTGGGGTGACCTGGCTAAAGAGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCAGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGTAGTAATAGAGACGCAGCTCCGCAATGTTGATCACAATGCCTTCGCGC  >  NC_000913/1169590‑1170075                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                ggCTGATGTACTTCAACCAGACGCGCACCGTTTGGTTCGGCAGAGACTTTTATCGGAGTGTTGATGATATTCACTTTGGTGCCTGGGGTGACCTGGCTAAAGAGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTAtccggtcc                                                                                                                                                                                                                                             >  1:248821/1‑251 (MQ=255)             tcactcgttcgtgactctttggggtCGGAAGAGACTTTGATCGGTGTGTTGATCATATTCACAGTGGGTCCTGGGGTGACCTGCCAAAAGATTGGTTTATTACTGTCACCCCGCTGACGAATACAGCAATAACTTTCCCCCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAT‑CGCCGCCATAGTCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGTTCCTGCCGGCACTa                                                                                                                                                                                                                                  <  2:53786/226‑1 (MQ=255)                            ccGTTTGGTTCGGCAGAGACTTTTATCGGAGTGTTGATTATATTTACTTTTGTTCCTGGGGTGACCTGGCTAAAGAGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAATTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCTGCCAGACGAAGCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAAt                                                                                                                                                                                                                  <  1:137176/251‑1 (MQ=255)                                      cgttctagaCTTTTTTCGGAGGGTTGATGATATTCCCTTGGGTGCGTGGGGGGACCTGGCTATAGAGTGTTTTGATATCGTCACCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCt                                                                                                                                                                                                        <  2:261448/245‑1 (MQ=255)                                           gagaCTTTTAGCGGATTGTTGTTGATATTCACTTTGGTGCCTGGGGTGGTCTGGCTAAAGAGTGTTTTGTTATCGTCAACCCGCAGACGATTACAGCCAAAACTTACCCTCATGCACAGGCCGAAATCGGCGTCCGTACCATGAAG‑AAATAAAACGCCGCCATAGGCCGCCAGACGAATCGCATGATTGCCCATTGGGTTATCCGGTCCAGCCGTCACTACCGCAGGCAACGCAATTCCCTGTGCTTtat                                                                                                                                                                                                    <  2:114178/250‑1 (MQ=255)                                            agaCTTTTATCGGAGTGTTGATGATATTCACTTTGGTGCCTGGGGTGACCTGGCTATAGAGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCt                                                                                                                                                                                                        >  1:261448/1‑245 (MQ=255)                                                            gtTGATGATATTCACTTTGGTGCCTGGGGTGACCTGGCTAAAGAGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CTCCGCCATAGGCCGCCAGACGAATCGCATTATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGttt                                                                                                                                                                                   <  1:188085/250‑1 (MQ=255)                                                               gatgatATTCACTTTGGTGCCTGGGGTGACCTGGCTAAAGAGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCAGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCg                                                                                                                                                                               >  1:263388/1‑251 (MQ=255)                                                                 tgatATTCACTTTGGTGCCTGGGGTGACCTGGCTAAAGAGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGACACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGtt                                                                                                                                                                             >  1:180852/1‑251 (MQ=255)                                                                             tgttGCCGGGGGTGACCGGGTAAAATATTGTGTTGATATCGTAATCCCGCAGACGAATCCAGCCAGAACTGTCCCGCATGCCAATGCCGAAAGCGGCGTTCGTACCATAAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCTATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGt                                                                                                                                                                  <  2:137856/247‑1 (MQ=255)                                                                             tGGTGCCTGGGGTGACCTGGCTAAAGCGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGtt                                                                                                                                                                 >  1:95481/1‑251 (MQ=255)                                                                                ggCCTGGGTGGACCTGGATAAAGAGTGTTTTGATAACGTCCCCCCGCAGACGAATACAGCCATAACTTACCCGCATGCCAATGCCGAAATCGGCTTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTggg                                                                                                                                                              <  2:143270/250‑1 (MQ=255)                                                                                                          gtTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACggtggt                                                                                                                                    <  1:2506/251‑1 (MQ=255)                                                                                                                           ccGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCa                                                                                                                   <  1:206218/251‑1 (MQ=255)                                                                                                                            cGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAACCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAg                                                                                                                  <  2:225974/251‑1 (MQ=255)                                                                                                                                      tACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTcacc                                                                                                         >  2:81675/1‑250 (MQ=255)                                                                                                                                      tACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTcacc                                                                                                         >  1:183733/1‑250 (MQ=255)                                                                                                                                        cAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCaccacc                                                                                                      >  1:28202/1‑251 (MQ=255)                                                                                                                                                    aCCCGCATGCCAATGCCGAAAGCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAt                                                                                          <  1:277882/251‑1 (MQ=255)                                                                                                                                                                                         gAAGCAAATAAA‑CGCCGCCATCGGAAGCCAGCCGAATCGCATGATGGAACATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCATGTTTGTCTGAAAAGGCGGTCACCATTGGCGGTGTCAACGTGTCACCACCTAACTGACCAATAACTATTGGGTACACGCGTACCGAATTTTTACCcggc                                                     >  2:176291/1‑251 (MQ=255)                                                                                                                                                                                                    a‑CGCCGCCATAGGCCGCCAGACGAATCGGATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGTAGTAATa                                          <  1:76262/251‑1 (MQ=255)                                                                                                                                                                                                             aTAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGGAGTAATAGAGACGc                                   >  1:233200/1‑250 (MQ=255)                                                                                                                                                                                                               aggtcgccAGACGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGTAGTAATAGAGACGCAg                                 <  1:220841/246‑1 (MQ=255)                                                                                                                                                                                                                          cGAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGTAGTAATAGAGACGCAGCTCCGCAATGtt                     <  1:240948/251‑1 (MQ=255)                                                                                                                                                                                                                           gAATCGCATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGTAGTAATAGAGACGCAGCTCCGCAATGTTg                    <  1:47149/251‑1 (MQ=255)                                                                                                                                                                                                                                 cATGATGGCCCATTGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGTAGTAATAGAGACGCAGCTCCGCAATGTTGATcaca              <  1:81675/251‑1 (MQ=255)                                                                                                                                                                                                                                              tGGGTTATCCGGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGTAGTAATAGAGACGCAGCTCCGCAATGTTGATCACAATGCCTTcgcgc  <  1:220558/250‑1 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                GGCTGATGTACTTCAACCAGACGCGCACCGTTTGGTTCGGCAGAGACTTTTATCGGAGTGTTGATGATATTCACTTTGGTGCCTGGGGTGACCTGGCTAAAGAGTGTTTTGATATCGTCATCCCGCAGACGAATACAGCCAGAACTTACCCGCATGCCAATGCCGAAATCGGCGTTCGTACCATGAAGCAAATAAA‑CGCCGCCATAGGCCGCCAGACGAATCGCATGATGGCCCATTGGGTTATCCAGTCCAGCCGGCACTACCGCAGGCAACTCAATTCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACCTATTGGATACACGGTTACCGAATTTTTACCCGGCGGGTAGTAATAGAGACGCAGCTCCGCAATGTTGATCACAATGCCTTCGCGC  >  NC_000913/1169590‑1170075

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: ‑