Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	2,180,816	T→C	Q11R (CAG→CGG)	U712_10915 ←	Uncharacterized protein ypjA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,180,816	0	T	C	100.0%	162.7 / NA	51	Q11R (CAG→CGG)	U712_10915	Uncharacterized protein ypjA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (23/28);  total (23/28)

GAAAAACGTTGCTGTCGGACTATCCGGAACAAAAATCAGGAAACGGGCCGGTGTCTCCAGTAGCTGCGGCAAGTACCAATAGTATCCGTATACCGTTCCCAGAAAATTGATGGCTAAGACAAGAATAAGCATCGGCTGCCGTCCTAATACATATTGAAACCATTTCACATCAAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATAAAAGTATATCCTTCCATTTTACAATTCA  >  CP006881/2180680‑2180950                                                                                                                                         |                                                                                                                                       taaaacCGTTGCTGGCGGCCTGTCCGCAACAAAAAGCAGGAACCGGGCCGGTGGCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      <  8:440211/138‑1 (MQ=255) gaaaAACGTTGCTGTCGGACTGTCCGGAACAAAAATCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      <  7:153073/139‑1 (MQ=255) caaacccGTGGCGGTGGGACTGTCCGGAAAAAAAAGCAGCCAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      <  7:183128/133‑1 (MQ=255) caaaaaCTTTGCGGGCGTCCTGGCCGTAAAAAAAAGCCGCACACGGGCCGGGGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      <  3:43811/138‑1 (MQ=255) caaaaaCGTTGCTGTGGGACTGTCCGGAACAAAAATCACGAACCGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCTATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      <  3:163374/138‑1 (MQ=255)           gCTGGCGGACGGTCCGGAACAAAAATCAGGAACCGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATa                                                                                                                            <  4:182062/139‑1 (MQ=255)            cTGTCGGACTGTCCGGAACAAAAATCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATa                                                                                                                            <  5:197631/138‑1 (MQ=255)            cTGTCGGACTGTCCGGAACAAAAATCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATa                                                                                                                            >  5:123287/1‑138 (MQ=255)                   aCTGTCCGGAACAAAAATCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGa                                                                                                                    <  3:317391/139‑1 (MQ=255)                    cttaccGAAACAAAAAACAGCAAACGGGCCTGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTA‑ACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGaaa                                                                                                                  <  5:435297/135‑1 (MQ=255)                       tCCGGAACAAAAATCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATGAGCATCGGCCGCTGCCCTAATACATATTGAAAc                                                                                                                 >  7:189548/1‑138 (MQ=255)                         cGGAACAAAAATCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTATCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCAt                                                                                                              >  3:384012/1‑139 (MQ=255)                          ggAAAAAAAATCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCAtt                                                                                                             <  4:367734/139‑1 (MQ=255)                           taaCAAAAATCTGCAACCGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCTTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCAttt                                                                                                            <  7:52047/138‑1 (MQ=255)                            aaCAAAAATCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCAttt                                                                                                            >  1:4007/1‑138 (MQ=255)                                aaacccAGTAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCAGTAAACCGTTCCCATAATATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACat                                                                                                       <  8:233786/134‑1 (MQ=255)                                aaacTCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACat                                                                                                       <  1:95195/139‑1 (MQ=255)                                 aaaTCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      <  6:223284/107‑1 (MQ=255)                                 aaaTCAGGAAACGGGCCGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      >  5:223284/1‑107 (MQ=255)                                 aaaTCAGGAAACGGGCCAGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      <  2:54769/107‑1 (MQ=255)                                 aaaTCAGGAAACGGGCCAGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      >  1:54769/1‑107 (MQ=255)                                                 cGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTc                                                                                      <  6:123287/139‑1 (MQ=255)                                                 cGGTGTCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTc                                                                                      <  4:180053/139‑1 (MQ=255)                                                     gtCTCCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTa                                                                                  <  7:171985/139‑1 (MQ=255)                                                       ctcCAAAAGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTaaa                                                                                <  5:187568/139‑1 (MQ=255)                                                          caaaaGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATGAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTaaaa                                                                               <  8:189548/133‑1 (MQ=255)                                                            aaaGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAaataa                                                                           <  2:98212/137‑1 (MQ=255)                                                              aGCTGCGGCAAGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAataata                                                                         >  4:213549/1‑139 (MQ=255)                                                                        aGTACCAATAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCatat                                                                >  1:411051/1‑138 (MQ=255)                                                                               aTAGTAGCCGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGc                                                        >  6:198439/1‑139 (MQ=255)                                                                                    agccGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACg                                                   >  7:22618/3‑139 (MQ=255)                                                                                    agccGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACg                                                   >  8:15046/3‑139 (MQ=255)                                                                                    agccGTAAACCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACg                                                   >  3:221755/3‑139 (MQ=255)                                                                                    agccGTAAACCGCTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      <  1:242481/54‑1 (MQ=255)                                                                                    agccGTAAACCGCTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGc                                                                                                                                      >  2:242481/3‑56 (MQ=255)                                                                                          aaaCCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGt                                             >  8:265483/3‑139 (MQ=255)                                                                                          aaaCCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGt                                             >  2:400597/3‑139 (MQ=255)                                                                                           aaCCGTTCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGt                                             >  8:267452/2‑138 (MQ=255)                                                                                                ttCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCtt                                       >  6:216266/1‑139 (MQ=255)                                                                                                ttCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCtt                                       >  2:240578/1‑139 (MQ=255)                                                                                                 tCCCAGAAAATTAATGGCTAAGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCttt                                      >  4:282989/1‑139 (MQ=255)                                                                                                             aaTGGCAAAGAAAATAATAAGCATCGGCCGCTGCCCTAATAAATATTCAAACCATTTCACATCCAATAAAATCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATaaaa                           <  2:4007/137‑1 (MQ=255)                                                                                                                ggCTAACACAAGAATAAGCTGCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCCAAACAACTCTCAGTCTGTAAAAAAAATATGTCAATAAAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATAAAAGta                        <  8:22618/138‑1 (MQ=255)                                                                                                                    aaGACAATAATACGCAGCGGCCGCTGCCCTAATACATATTCAAACAATTTCACATCGAATCAACTCTCAGTCTGAAAAAATAATATGTCAATATAAAAACGCTGACGCCGGGTCAGCTTTTGATAATAAAAGTATATcc                   <  1:240578/139‑1 (MQ=255)                                                                                                                    aaGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATAAAAGTATATcc                   >  5:81671/1‑139 (MQ=255)                                                                                                                     aGACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTTTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATAAAAGTATATcc                   <  7:267452/138‑1 (MQ=255)                                                                                                                      gACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTc                                                                                      >  6:303079/1‑70 (MQ=255)                                                                                                                      gACAAGAATAAGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTc                                                                                      <  5:303079/70‑1 (MQ=255)                                                                                                                         aaGAATAACCATCGGCCGCTGCCATAAAAAATATTGAAACCATTTCACATCTAATCAACTCTCTGTCTTTAAAAATAATATGTCAATATAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATAAAAGTATATCCTTCCa              <  6:81671/139‑1 (MQ=255)                                                                                                                                aGCATCGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATAAAAGTATATCCTTCCATTTGAc        >  3:160945/1‑138 (MQ=255)                                                                                                                                     cGGCCGCTGCCCTAATACATATTGAAACCATTTCACATCGAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATAAAAGTATATCCTTCCATTTGACAATTca  >  5:154380/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                       GAAAAACGTTGCTGTCGGACTATCCGGAACAAAAATCAGGAAACGGGCCGGTGTCTCCAGTAGCTGCGGCAAGTACCAATAGTATCCGTATACCGTTCCCAGAAAATTGATGGCTAAGACAAGAATAAGCATCGGCTGCCGTCCTAATACATATTGAAACCATTTCACATCAAATCAACTCTCAGTCTGTAAAAATAATATGTCCATATAAAAAAGCTGACGCCGGGTCAGCTTTTGATAATAAAAGTATATCCTTCCATTTTACAATTCA  >  CP006881/2180680‑2180950

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑