Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,913,654	T→C	intergenic (‑3/+45)	relA ← / ← rlmD	(p)ppGpp synthetase I/GTP pyrophosphokinase/23S rRNA m(5)U1939 methyltransferase, SAM‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,913,654	0	T	C	100.0%	179.9 / NA	50	intergenic (‑3/+45)	relA/rlmD	(p)ppGpp synthetase I/GTP pyrophosphokinase/23S rRNA m(5)U1939 methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/25);  total (25/25)

GTTGCAGACAATACGCCCAGGTTTCGGCTAAGCACTCACACGACTTCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGTCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAACTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATA  >  NC_000913/2913519‑2913785                                                                                                                                        |                                                                                                                                    gTTGCAGACAATACGCCCAGGTTTCGGCTAAGCACTCACACGACTTCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCct                                                                                                                                  <  2:134758/139‑1 (MQ=255)        aCAATACGCCCAGGTTTCGGCTAAGCACTCACACGACTTCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCttt                                                                                                                           >  1:150456/1‑139 (MQ=255)          aaTACGCCCAGGTTTCGGCTAAGCACTCACACGACTTCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAg                                                                                                                         >  2:582972/1‑139 (MQ=255)                      tttCGGCTAAGCACTCACACGACTTCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTg                                                                                                             <  2:338613/139‑1 (MQ=255)                                       cacGACTTCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCg                                                                                            <  2:574692/139‑1 (MQ=255)                                         cGACTTCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCa                                                                                          <  2:890436/139‑1 (MQ=255)                                              tCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTAt                                                                                     >  2:555567/1‑139 (MQ=255)                                                       tAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAAt                                                                                              >  2:809398/1‑121 (MQ=255)                                                       tAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAAt                                                                                              <  1:809398/121‑1 (MQ=255)                                                            cccAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTa                                                                                                                          >  2:32231/1‑88 (MQ=255)                                                            cccAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTa                                                                                                                          <  1:32231/88‑1 (MQ=255)                                                                 aCTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAGTCGCAATTATTTAAcg                                                                               >  1:630005/1‑126 (MQ=255)                                                                 aCTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAAcg                                                                               <  2:630005/126‑1 (MQ=255)                                                                     gCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCct                                                                                                                                  <  2:548438/71‑1 (MQ=255)                                                                     gCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCct                                                                                                                                  >  1:548438/1‑71 (MQ=255)                                                                     gCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCAt                                                              >  1:483324/1‑139 (MQ=255)                                                                                                ccAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGaa                                   >  2:489891/1‑139 (MQ=255)                                                                                                ccAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGaa                                   >  2:465396/1‑139 (MQ=255)                                                                                                              atGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCg                     >  2:843372/1‑139 (MQ=255)                                                                                                               tgtgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGc                    >  1:821664/1‑139 (MQ=255)                                                                                                                 tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGc                                                                                                  >  1:633756/1‑59 (MQ=255)                                                                                                                 tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGc                                                                                                  <  2:633756/59‑1 (MQ=255)                                                                                                                 tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCg                                                                                            >  2:610403/1‑65 (MQ=255)                                                                                                                 tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCg                                                                                            <  1:610403/65‑1 (MQ=255)                                                                                                                 tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCgt                                            >  2:480467/1‑113 (MQ=255)                                                                                                                 tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCgt                                            <  1:480467/113‑1 (MQ=255)                                                                                                                 tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCa                  >  2:903120/1‑139 (MQ=255)                                                                                                                 tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCa                  >  2:407596/1‑139 (MQ=255)                                                                                                                  gCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGTACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCgtg                                           <  2:665765/113‑1 (MQ=255)                                                                                                                  gCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCgtg                                           >  1:665765/1‑113 (MQ=255)                                                                                                                  gCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAg                 >  2:83798/1‑139 (MQ=255)                                                                                                                   cACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGt                <  1:903120/139‑1 (MQ=255)                                                                                                                    aCTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGAt                                                          >  2:791428/1‑96 (MQ=255)                                                                                                                    aCTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGAt                                                          <  1:791428/96‑1 (MQ=255)                                                                                                                     cttcttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTcg              <  2:150456/139‑1 (MQ=255)                                                                                                                      ttcttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGATCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCa                           <  1:332317/125‑1 (MQ=255)                                                                                                                      ttcttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGATCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCa                           >  2:332317/1‑125 (MQ=255)                                                                                                                       tcttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTcgcg            <  1:59744/139‑1 (MQ=255)                                                                                                                       tcttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTcgcg            <  1:83798/139‑1 (MQ=255)                                                                                                                         ttACCGCAACCATTGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa          <  1:177701/139‑1 (MQ=255)                                                                                                                         ttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa          <  2:821664/139‑1 (MQ=255)                                                                                                                         ttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa          <  2:483324/139‑1 (MQ=255)                                                                                                                           aCCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCgg                                                                                                   >  2:725822/1‑48 (MQ=255)                                                                                                                           aCCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCgg                                                                                                   <  1:725822/48‑1 (MQ=255)                                                                                                                                aaCCATCGCCCTCTCCTTTAGGGATCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGtat   >  1:567792/1‑139 (MQ=255)                                                                                                                                 aCCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGtata  <  2:129241/139‑1 (MQ=255)                                                                                                                                  ccATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAAc                                  >  2:132418/1‑106 (MQ=255)                                                                                                                                  ccATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAAc                                  <  1:132418/106‑1 (MQ=255)                                                                                                                                  ccATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa          >  1:88445/1‑130 (MQ=255)                                                                                                                                  ccATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa          <  2:88445/130‑1 (MQ=255)                                                                                                                                        |                                                                                                                                    GTTGCAGACAATACGCCCAGGTTTCGGCTAAGCACTCACACGACTTCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGTCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAACTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATA  >  NC_000913/2913519‑2913785

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑