Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,008,583	C→T	30.9%	Q253* (CAA→TAA)	yhiJ →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,008,583	0	C	T	30.9%	97.5 / 55.9	68	Q253* (CAA→TAA)	yhiJ	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (31/16);  new base T (9/12);  total (40/28)
Fisher's exact test for biased strand distribution p-value = 1.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

TCCTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGAAAGTCT  >  W3110S.gb/4008515‑4008650                                                                     |                                                                    tCCTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGc                                                                     <  1:2986908/69‑1 (MQ=255) tCCTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGc                                                                     <  1:1575662/69‑1 (MQ=255)  ccTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCa                                                                    >  1:1177534/1‑69 (MQ=255)        ccAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACtt                                                                <  1:304370/67‑1 (MQ=255)        ccAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACtt                                                                <  1:1206299/67‑1 (MQ=255)         cAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTaa                                                              <  1:2887283/68‑1 (MQ=255)         cAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTa                                                               <  1:2772916/67‑1 (MQ=255)             tGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTa                                                         >  1:938522/1‑69 (MQ=255)              gCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTaa                                                        >  1:378633/1‑69 (MQ=255)              gCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTaa                                                        >  1:2333169/1‑69 (MQ=255)              gCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTaa                                                        >  1:1176284/1‑69 (MQ=255)              gCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTaa                                                              <  1:1884195/63‑1 (MQ=255)              gCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTaa                                                              <  1:1491824/63‑1 (MQ=255)                      taGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACt                                                          <  1:1239431/59‑1 (MQ=255)                      taGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACt                                                          <  1:199005/59‑1 (MQ=255)                      taGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAAt                                                 >  1:595818/1‑68 (MQ=255)                      taGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAAt                                                 >  1:1239137/1‑68 (MQ=255)                      taGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAAt                                                 >  1:1887725/1‑68 (MQ=255)                      taGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAAt                                                 >  1:2231242/1‑68 (MQ=255)                      taGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAAt                                                 >  1:2492693/1‑68 (MQ=255)                        gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGtt                                                    >  1:1534429/1‑63 (MQ=255)                        gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGtt                                                    >  1:1219491/1‑63 (MQ=255)                        gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATAc                                               >  1:15126/1‑68 (MQ=255)                        gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATAc                                               >  1:1671520/1‑68 (MQ=255)                        gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATAc                                               >  1:794499/1‑68 (MQ=255)                        gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATAc                                               >  1:139843/1‑68 (MQ=255)                              gAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaat                                            <  1:2583483/65‑1 (MQ=255)                              gAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaat                                            <  1:2391055/65‑1 (MQ=255)                                    ctcAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATc                                  >  1:2987/1‑69 (MQ=255)                                      cAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATcc                                 >  1:1330998/1‑68 (MQ=255)                                         cGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTg                               <  1:1163571/67‑1 (MQ=255)                                         cGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGaa                             <  1:2142438/69‑1 (MQ=255)                                          gTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTg                               >  1:2719129/1‑66 (MQ=255)                                             ttGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAAc                            >  1:45060/1‑66 (MQ=255)                                              tGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                          >  1:2415472/1‑67 (MQ=255)                                               gCTAAGGGATAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaa                        <  1:3201444/68‑1 (MQ=255)                                               gCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaag                       <  1:503917/69‑1 (MQ=255)                                               gCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                          >  1:3282815/1‑66 (MQ=255)                                               gCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                          >  1:738485/1‑66 (MQ=255)                                               gCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                          >  1:3030362/1‑66 (MQ=255)                                               gCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                          >  1:929735/1‑66 (MQ=255)                                               gCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                          >  1:2615924/1‑66 (MQ=255)                                               gCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                          >  1:1707165/1‑66 (MQ=255)                                               gCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                          >  1:1353438/1‑66 (MQ=255)                                                cTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaa                        <  1:899233/67‑1 (MQ=255)                                                 tAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaaga                      <  1:1036772/68‑1 (MQ=255)                                                 tAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaaga                      <  1:3348047/68‑1 (MQ=255)                                                     ggAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACat                 <  1:849979/69‑1 (MQ=255)                                                     ggAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACat                 <  1:2882557/69‑1 (MQ=255)                                                     ggAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACat                 >  1:3480476/1‑69 (MQ=255)                                                          aCTTTAATGAGCAACTTAACACTAATGTTAATACaat                                            <  1:1031635/37‑1 (MQ=255)                                                           cTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACattat              >  1:470314/1‑66 (MQ=255)                                                           cTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaa                        >  1:1415962/1‑56 (MQ=255)                                                           cTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACattat              >  1:680216/1‑66 (MQ=255)                                                            tttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTAtttt           >  1:3267557/1‑68 (MQ=255)                                                            tttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTAtttt           >  1:454866/1‑68 (MQ=255)                                                            tttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTAtttt           >  1:483456/1‑68 (MQ=255)                                                             ttAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTAttt            >  1:2789490/1‑66 (MQ=255)                                                             ttAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTa          >  1:309529/1‑68 (MQ=255)                                                             ttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                                     <  1:1421815/41‑1 (MQ=255)                                                             ttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                                     <  1:734025/41‑1 (MQ=255)                                                             ttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                                     <  1:2456439/41‑1 (MQ=255)                                                             ttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                                     <  1:1524478/41‑1 (MQ=255)                                                             ttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                                     <  1:3577791/41‑1 (MQ=255)                                                             ttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                                     <  1:3414549/41‑1 (MQ=255)                                                             ttAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                                     <  1:2472011/41‑1 (MQ=255)                                                              tAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTa          >  1:3500672/1‑67 (MQ=255)                                                              tAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTa          >  1:2799070/1‑67 (MQ=255)                                                              tAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTa          >  1:2871468/1‑67 (MQ=255)                                                                aTGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGa        <  1:2310264/67‑1 (MQ=255)                                                                     cAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGAAAGTCt  <  1:2471688/68‑1 (MQ=255)                                                                     |                                                                    TCCTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGAAAGTCT  >  W3110S.gb/4008515‑4008650

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑