Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	2,912,587	C→A	W355C (TGG→TGT)	relA ←	(p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	2,912,587	0	C	A	97.7%	127.6 / NA	44	W355C (TGG→TGT)	relA	(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (24/19);  minor base G (0/1);  total (24/20)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTCCAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGACGTAATCGTCAA  >  NC_000913_3_pae_tpiA/2912441‑2912732                                                                                                                                                   |                                                                                                                                                  tcgtcAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACa                                                                                                                                                 <  1:384991/149‑1 (MQ=255)      aaaGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTgcg                                                                                                                                            >  2:111524/1‑149 (MQ=255)                cTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACAcc                                                                                                                                  <  1:111524/149‑1 (MQ=255)                      aCTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAAGCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCCCTTTAAATTGATAGAGCGCAGCAAGACCCAGctc                                                                                                                            >  1:145357/1‑149 (MQ=255)                           gtcgAGCATTTAGCCGGAATCAGACATCTCTACCTGCCACGCAAGCAGTGTACGCAGCAAGGCAATCGGGTCTTCATGTCCCGAACGTGCGCCACCAGCAGCCGCGCCCTCTTTATATTTACAGTACGCAGCAAcaaccaaccttacgt                                                                                                                       >  2:457731/1‑142 (MQ=255)                                gCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCa                                                                                                                  <  1:242348/149‑1 (MQ=255)                                 cATTTCGCGGGAATCAGCCATCTCTTTCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCAt                                                                                                                 <  2:500781/149‑1 (MQ=255)                                    ttCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCa                                                                                                              >  2:232462/1‑149 (MQ=255)                                         cGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGt                                                                                                         <  1:876638/149‑1 (MQ=255)                                         cGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGt                                                                                                         >  1:844506/1‑149 (MQ=255)                                           gAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCCTCTGttt                                                                                                       >  1:964173/1‑149 (MQ=255)                                           gAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGttt                                                                                                       <  1:232462/149‑1 (MQ=255)                                              tCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCGGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGt                                                                                                    >  1:219869/1‑149 (MQ=255)                                                  ccATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCAt                                                                                                                 >  2:884864/1‑132 (MQ=255)                                                  ccATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCAt                                                                                                                 <  1:884864/132‑1 (MQ=255)                                                  ccATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCgg                                                                                                >  1:795899/1‑149 (MQ=255)                                                       tctTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTCCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTg                                                                                           >  1:1027438/1‑149 (MQ=255)                                                               ccACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGCTCTCaa                                                                                   >  1:667558/1‑149 (MQ=255)                                                                         aGTTTACGCAGCCAGGCCATCCGGTCTTCATGTCCCGAACGTGCGCCGCCACCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCCTCTGTTTGGTGCGGAGTTGGATCTCAACGGTATTTcc                                                                         >  2:556676/1‑149 (MQ=255)                                                                           tttACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGCTTTGGATCTCAACGGTTTTTCCAc                                                                       >  1:247393/1‑149 (MQ=255)                                                                           tttACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATACATCTGTTTGGTGCGGATTTGGAGCTCAACGGTTTTTCTAc                                                                       >  1:477593/1‑149 (MQ=255)                                                                            ttACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCAcc                                                                      <  2:795899/149‑1 (MQ=255)                                                                             ttcGCACCCAGGCATGTCGGTTCTTATGCTCCGACCGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTTGTGCGGATTTGGATCTCAACGGTTTTTCCAccc                                                                     <  2:1061341/147‑1 (MQ=255)                                                                                    ccAGGCAATCCGGTCTTCATGTCCCGCACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATAAACAGTGCGCAGCAACAACCAACCCTGCATCTTCCTGCCTCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCa                                                              >  1:1088472/1‑149 (MQ=255)                                                                                    ccAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCAGCCGGCCCCa                                                              >  2:848737/1‑149 (MQ=255)                                                                                      aGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCCTCTTCATGCATCTGGTTGGTGCGGATTTGGATCTCAACGGATTGTCCCCCCGGCCCCCGa                                                            >  2:80310/1‑149 (MQ=255)                                                                                           aacccggcTTCGTGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATACTGACAGTGCGCAGCAACACCCAACTCTGCATCTTCATTCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCAc                                                       <  1:385638/142‑1 (MQ=255)                                                                                            ttcGGTCTTCATGTCGCGACCGCGCGCCGGCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCCACGGTTTTTCCACCCGGCCCCAACACCACg                                                      <  2:12158/147‑1 (MQ=255)                                                                                                        gTCCCGCACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGAc                                          <  2:197022/149‑1 (MQ=255)                                                                                                        gTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGAc                                          <  1:729417/149‑1 (MQ=255)                                                                                                         tCCCGAAAGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAGCACCCAACTCTGCATCTTCATGAATCTGTTTGGTGCGGATGTGGATCTCAACGGTATTTCCACCCGGCTCCAGAACCACGGTATGAATAGACt                                         >  1:1052281/1‑149 (MQ=255)                                                                                                           ccGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCACAGAACCACGGTATGAATAGACTGa                                       >  1:1047607/1‑149 (MQ=255)                                                                                                               aCGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAAc                                   <  2:964173/149‑1 (MQ=255)                                                                                                                   gcgcCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGtt                               <  2:989034/149‑1 (MQ=255)                                                                                                                          cagcagCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTc                        >  1:911076/1‑149 (MQ=255)                                                                                                                           agcagcCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCg                       >  2:413098/1‑149 (MQ=255)                                                                                                                                    gctcttgttATAGTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGa              <  2:913656/142‑1 (MQ=255)                                                                                                                                    gcCCTCCTTATATTTACAGTGCGCAGCAACACCCAACTCTGCAGCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGTTTTCGGGTTAGCGa              <  1:690406/149‑1 (MQ=255)                                                                                                                                     cccTTTTGATATTCGCAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGAc             <  2:888966/149‑1 (MQ=255)                                                                                                                                          tttATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATaa                                    >  2:427855/1‑121 (MQ=255)                                                                                                                                          tttATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATaa                                    <  1:427855/121‑1 (MQ=255)                                                                                                                                           ttATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGACGTAATc       >  1:753065/1‑149 (MQ=255)                                                                                                                                                tttACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGACGTAATCGTCaa  >  2:342984/1‑149 (MQ=255)                                                                                                                                                tttACAGTGAGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACACGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGAAGTAATctccaa  <  2:481609/149‑6 (MQ=255)                                                                                                                                                   |                                                                                                                                                  TCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTCCAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGACGTAATCGTCAA  >  NC_000913_3_pae_tpiA/2912441‑2912732

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑