Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,248,192	A→T	L114Q (CTG→CAG)	lysP ←	lysine transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,192	0	A	T	98.1%	171.6 / ‑4.1	52	L114Q (CTG→CAG)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (22/29);  total (23/29)
Fisher's exact test for biased strand distribution p-value = 4.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.24e-01

GTTCAGCAGGAAGATAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCAGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCTGACCGTAAGTGGCAA  >  NC_000913/2248098‑2248288                                                                                               |                                                                                                 gTTCAGCAGGAAGATAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCa                                                                                             >  1:1247012/1‑100 (MQ=255)    cagcagGAAGATAACGCCGAGGAACAACGCACTCCAGATCCAGACCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGt                                                                                               >  1:567207/1‑95 (MQ=255)      gcagGAAGATAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGc                                                                                        >  2:445504/1‑100 (MQ=255)      gcagGAAGATAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGc                                                                                        <  2:664128/100‑1 (MQ=255)      gcagGAAGATAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCAGGTCAACGGc                                                                                        >  2:575919/1‑100 (MQ=255)          gAAGATAACGCCGAGGCACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATa                                                                                    <  1:1095431/100‑1 (MQ=255)           aaGATAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAg                                                                                   >  2:357804/1‑100 (MQ=255)            aGATAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGCACCACCAGCTCATGACCACCTGAGCTGCAACCTGGTCAACGGCGATAGt                                                                                  >  2:228357/1‑100 (MQ=255)              aTAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCa                                                                                >  1:745018/1‑100 (MQ=255)               cgatctcGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCAc                                                                               <  2:265764/94‑1 (MQ=255)                  cGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGc                                                                            >  2:540155/1‑100 (MQ=255)                     cGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCAcagatcg                                                                         >  1:265767/1‑94 (MQ=255)                       aagaagaaCGCACTGGAGATCGAGCCCGGTGTATCCGGGAAGCAGCAGGTCATGACCAGCTGAGCTGCAACCTGGTTAACGGGGATAGTCAcc                                                                              <  2:1232917/91‑1 (MQ=255)                         gAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTg                                                                     <  2:218494/100‑1 (MQ=255)                          aacaacGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGTTCAACGGCGATAGTCACCGCCCAGTTGt                                                                    <  2:1205826/100‑1 (MQ=255)                          aacaacGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGt                                                                    >  2:80024/1‑100 (MQ=255)                            caacGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTAc                                                                  <  2:362185/100‑1 (MQ=255)                             aacGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTAcc                                                                 <  1:404797/100‑1 (MQ=255)                             aacGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTAcc                                                                 >  1:314206/1‑100 (MQ=255)                             aacGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTAcc                                                                 <  2:323345/100‑1 (MQ=255)                             aacGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTAcc                                                                 <  2:1249502/100‑1 (MQ=255)                              acGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCa                                                                <  2:71907/100‑1 (MQ=255)                              acGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCa                                                                >  2:1289440/1‑100 (MQ=255)                               cGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCag                                                               <  1:1303406/100‑1 (MQ=255)                                 cACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCagt                                                              >  1:127649/1‑99 (MQ=255)                                  aCTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCagtag                                                            >  1:50349/1‑100 (MQ=255)                                    tCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGtt                                                          >  2:84377/1‑100 (MQ=255)                                        gATCCAGCCCGGTGTATCCGGGAACCCCCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTccag                                                      <  1:516799/100‑1 (MQ=255)                                         aTCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTccagc                                                     <  1:84379/100‑1 (MQ=255)                                         aTCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTccagc                                                     <  2:919693/100‑1 (MQ=255)                                          tCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTccagc                                                     >  2:966143/1‑99 (MQ=255)                                                 cGGTGTATCCGGGAACCACCAGCTCATGACCAGCCGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAgcgc                                              <  2:877233/99‑1 (MQ=255)                                                     gtATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGc                                         <  1:1079623/100‑1 (MQ=255)                                                        tCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCaa                                      >  1:212613/1‑100 (MQ=255)                                                         ccGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACGTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCaaa                                     >  2:695110/1‑100 (MQ=255)                                                          cGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAg                                    <  2:1178267/100‑1 (MQ=255)                                                          cGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAg                                    <  2:652278/100‑1 (MQ=255)                                                          cGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAg                                    <  2:5892/100‑1 (MQ=255)                                                               accaccAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCcttc                               <  1:1011954/100‑1 (MQ=255)                                                               accaccAGCTCATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGGTGTACCAGTAGTTCCAGCCGAGCGCGAAGCCAAAGccct                                >  2:533804/1‑97 (MQ=255)                                                                         cATGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAg                     >  2:547228/1‑100 (MQ=255)                                                                          aTGACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGt                    <  1:606142/100‑1 (MQ=255)                                                                            gACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTc                  <  2:1302404/100‑1 (MQ=255)                                                                            gACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTc                  <  1:973976/100‑1 (MQ=255)                                                                            gACCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTc                  >  1:512885/1‑100 (MQ=255)                                                                             aCCAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCt                 >  2:230440/1‑100 (MQ=255)                                                                              ccAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCTg                <  2:21996/100‑1 (MQ=255)                                                                              ccAGCTGAGCTGCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCTg                <  2:22597/100‑1 (MQ=255)                                                                                agctgagctgCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCTGAc              <  2:93458/100‑1 (MQ=255)                                                                                  ctgagctgCAACCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCTGACCg            <  2:931461/100‑1 (MQ=255)                                                                                           aaCCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCTGACCGTAAGTGGCa   <  2:464400/100‑1 (MQ=255)                                                                                            aCCTGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCTGACCGTAAGTGGCaa  >  2:1154146/1‑100 (MQ=255)                                                                                               |                                                                                                 GTTCAGCAGGAAGATAACGCCGAGGAACAACGCACTCCAGATCCAGCCCGGTGTATCCGGGAACCACCAGCTCATGACCAGCTGAGCTGCAACCAGGTCAACGGCGATAGTCACCGCCCAGTTGTACCAGTAGTTCCAGCCCAGCGCGAAGCCAAAGCCTTCTTCAACATAGTTCTGACCGTAAGTGGCAA  >  NC_000913/2248098‑2248288

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑