Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,362,267	T→G	42.7%	E344A (GAA→GCA)	cadA ←	lysine decarboxylase 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,362,267	0	T	G	42.7%	0.2 / 102.2	68	E344A (GAA→GCA)	cadA	lysine decarboxylase 1
Reads supporting (aligned to +/- strand):  ref base T (25/14);  new base G (14/15);  total (39/29)
Fisher's exact test for biased strand distribution p-value = 2.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGT  >  W3110S.gb/4362201‑4362335                                                                   |                                                                     tgAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTa                                                                  <  1:1190824/71‑1 (MQ=255) tgAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTa                                                                  <  1:425064/71‑1 (MQ=255)     tGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATc                                                              <  1:708723/71‑1 (MQ=255)       gACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCg                                                             <  1:717063/70‑1 (MQ=255)            ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTgag                                                        >  1:2441853/1‑70 (MQ=255)            ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTgag                                                        >  1:2182978/1‑70 (MQ=255)            ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCg                                                             >  1:3768217/1‑65 (MQ=255)            ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTgag                                                        >  1:3728915/1‑70 (MQ=255)            ggTTTCGTAAATCACTTTCCCTTCTACAAGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTgag                                                        >  1:443657/1‑70 (MQ=255)                tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt                                                   >  1:922283/1‑71 (MQ=255)                tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt                                                   >  1:2651945/1‑71 (MQ=255)                tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt                                                   >  1:3340154/1‑71 (MQ=255)                tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGt                                                    <  1:3084460/70‑1 (MQ=255)                     aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtgt                                              <  1:38454/71‑1 (MQ=255)                     aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATc                                                              >  1:685918/1‑55 (MQ=255)                     aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATc                                                              >  1:2506383/1‑55 (MQ=255)                      aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa                                             <  1:1512271/71‑1 (MQ=255)                      aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa                                             <  1:2922305/71‑1 (MQ=255)                      aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa                                             <  1:706283/71‑1 (MQ=255)                      aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa                                             <  1:574036/71‑1 (MQ=255)                      aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa                                             <  1:1291971/71‑1 (MQ=255)                       tCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt                                                   <  1:1131424/64‑1 (MQ=255)                         aCTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAgg                                          <  1:2338781/71‑1 (MQ=255)                          cTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGc                                         <  1:3653497/71‑1 (MQ=255)                               ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa                                    >  1:1331661/1‑71 (MQ=255)                               ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa                                    >  1:3239856/1‑71 (MQ=255)                               ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa                                    >  1:2922572/1‑71 (MQ=255)                               ccTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa                                    <  1:3311922/71‑1 (MQ=255)                               ccTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa                                    <  1:318095/71‑1 (MQ=255)                                      cacGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCAcgcg                                <  1:3228256/68‑1 (MQ=255)                                      cacGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAg                             >  1:2323106/1‑71 (MQ=255)                                         ggCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa                          <  1:132007/71‑1 (MQ=255)                                         ggCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa                          <  1:3495092/71‑1 (MQ=255)                                         ggCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa                          <  1:3228847/71‑1 (MQ=255)                                         ggCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa                          <  1:196573/71‑1 (MQ=255)                                          gCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa                         <  1:3011612/71‑1 (MQ=255)                                          gCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa                         <  1:3812125/71‑1 (MQ=255)                                            cACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTa                                             <  1:2546045/49‑1 (MQ=255)                                             aCCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGt                      >  1:4078803/1‑71 (MQ=255)                                                gCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                   >  1:1265889/1‑71 (MQ=255)                                                gCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                   >  1:2502468/1‑71 (MQ=255)                                                 cTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAgg                                          <  1:2952766/47‑1 (MQ=255)                                                 cTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAgg                                          <  1:3584495/47‑1 (MQ=255)                                                   cATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCa                                        >  1:341657/1‑47 (MQ=255)                                                      aCCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTaa                                            >  1:3073677/1‑40 (MQ=255)                                                      aCCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa                        >  1:3157642/1‑60 (MQ=255)                                                      aCCGCATTTACATTCGTAAATCGGTGAGAAGTTGGTGTaa                                            >  1:1100546/1‑40 (MQ=255)                                                       ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAtt             >  1:1968202/1‑70 (MQ=255)                                                       ccGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTaa                                            >  1:2107495/1‑39 (MQ=255)                                                        cGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatgg                <  1:112867/66‑1 (MQ=255)                                                        cGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatgg                <  1:2037364/66‑1 (MQ=255)                                                         gCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca          >  1:1757102/1‑71 (MQ=255)                                                         gCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca          >  1:2592196/1‑71 (MQ=255)                                                         gCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTggatggat              >  1:2045108/1‑67 (MQ=255)                                                          cATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTggatggat              >  1:2465077/1‑66 (MQ=255)                                                          cATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTggatggat              >  1:3903628/1‑66 (MQ=255)                                                          cATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca          >  1:44845/1‑70 (MQ=255)                                                            tttACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACAt       >  1:2289126/1‑71 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa                                    >  1:484831/1‑40 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa                        >  1:2799045/1‑52 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa                        >  1:2848326/1‑52 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa                        >  1:3219242/1‑52 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa                          >  1:1144805/1‑50 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAg                       >  1:427565/1‑53 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAg                       >  1:143063/1‑53 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATc      >  1:4017136/1‑70 (MQ=255)                                                              tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATc      >  1:1829940/1‑70 (MQ=255)                                                                 cTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAgt  <  1:36481/71‑1 (MQ=255)                                                                   |                                                                     TGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGT  >  W3110S.gb/4362201‑4362335

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑