Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 683,687 C→A 27.7% A10S (GCG→TCG)  mgsA ← methylglyoxal synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE683,6870CA27.7% 159.8 / 57.6 108A10S (GCG→TCG) mgsAmethylglyoxal synthase
Reads supporting (aligned to +/- strand):  ref base C (15/63);  new base A (5/25);  total (20/88)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01

Only 100 of 115 total aligned reads displayed.

CCACCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTA  >  minE/683624‑683753
                                                               |                                                                  
ccACCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGAAgg                                                                 >  1:2688316/1‑67 (MQ=255)
ccACCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGAAgg                                                                 >  1:2460309/1‑67 (MQ=255)
ccACCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGAAgg                                                                 >  1:3341835/1‑67 (MQ=255)
ccACCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAAAATGTTTCCGCGAAgg                                                                 >  1:3310172/1‑67 (MQ=255)
              aGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               >  1:2114412/1‑55 (MQ=255)
              aGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAgtcgtc                                                 >  1:1723650/1‑69 (MQ=255)
              aGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAgtcgtc                                                 >  1:1210634/1‑69 (MQ=255)
              aGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAgtcgtc                                                 <  1:128191/69‑1 (MQ=255)
              aGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAgtcgtc                                                 >  1:116392/1‑69 (MQ=255)
              aGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAgtcgtc                                                 >  1:1889012/1‑69 (MQ=255)
              aGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAgtcgtc                                                 >  1:1345096/1‑69 (MQ=255)
                    tgtttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               <  1:2143987/49‑1 (MQ=255)
                    tgtttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               <  1:3348497/49‑1 (MQ=255)
                    tgtttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               <  1:1887670/49‑1 (MQ=255)
                    tgtttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               <  1:3266845/49‑1 (MQ=255)
                    tgtttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               <  1:3217855/49‑1 (MQ=255)
                    tgtttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               <  1:1433103/49‑1 (MQ=255)
                    tgtttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               <  1:69589/49‑1 (MQ=255)
                    tgtttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTa                                                               <  1:2355587/49‑1 (MQ=255)
                       ttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCAt                                         <  1:2003035/68‑1 (MQ=255)
                       ttgCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCAt                                         <  1:310964/68‑1 (MQ=255)
                           aGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATg                                     <  1:1174578/68‑1 (MQ=255)
                           aGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATg                                     <  1:214727/68‑1 (MQ=255)
                           aGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATg                                     <  1:3130631/68‑1 (MQ=255)
                           aGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATg                                     <  1:2606331/68‑1 (MQ=255)
                           aGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATg                                     <  1:3360276/68‑1 (MQ=255)
                                 cGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATc                               >  1:1323918/1‑68 (MQ=255)
                                    gtgCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGt                            <  1:836953/68‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:2852398/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:2968602/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:2976615/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:300176/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:2546766/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:1316120/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:1426542/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:500901/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:2795426/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:1899189/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:3409607/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:1568195/69‑1 (MQ=255)
                                       ccaccaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGtt                        <  1:1701505/69‑1 (MQ=255)
                                         accaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTa                       <  1:1448884/68‑1 (MQ=255)
                                         accaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTa                       <  1:1298486/68‑1 (MQ=255)
                                         accaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTa                       <  1:720675/68‑1 (MQ=255)
                                         accaGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTa                       <  1:1012628/68‑1 (MQ=255)
                                           caGGGCAATTTGTTTCCGCGAAGGTAAAGTGCGAGTGGTCAGTTCCATAATGTACATCCGTa                           <  1:2309881/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:828858/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:2692927/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:840967/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:2870323/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:2962935/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:3035069/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:451861/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:401905/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:2476785/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:3387714/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:222869/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:2646358/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:1129150/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:2253036/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:1566062/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:1288703/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:1325581/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:19296/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:2343218/62‑1 (MQ=255)
                                           caGCGCAATATGTTTCCGCGAAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:2375431/62‑1 (MQ=255)
                                               gcAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTcc                >  1:597189/1‑69 (MQ=255)
                                               gcAATATGTTTCCGCGAATGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTa                           <  1:473907/58‑1 (MQ=255)
                                                 aaTATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTa              <  1:3006408/69‑1 (MQ=255)
                                                 aaTATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTa              <  1:1471099/69‑1 (MQ=255)
                                                 aaTATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTa              <  1:1823980/69‑1 (MQ=255)
                                                  atatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTcc                >  1:1901044/1‑66 (MQ=255)
                                                  atatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTcc                >  1:2309284/1‑66 (MQ=255)
                                                  atatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTACAt                                         >  1:2841564/1‑41 (MQ=255)
                                                  atatGTTTCCGCGCAGGTAAAGTGCGAGTCGTAAGTTCCATAATGTACATCCGTAGtt                        <  1:824797/58‑1 (MQ=255)
                                                   tatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACa            <  1:1509784/69‑1 (MQ=255)
                                                   tatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACa            <  1:1874093/69‑1 (MQ=255)
                                                   tatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACa            <  1:1688570/69‑1 (MQ=255)
                                                   tatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACa            <  1:3040164/69‑1 (MQ=255)
                                                   tatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACa            <  1:2312938/69‑1 (MQ=255)
                                                   tatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACa            <  1:2944517/69‑1 (MQ=255)
                                                   tatGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACa            <  1:2476080/69‑1 (MQ=255)
                                                    atGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAg           >  1:1739109/1‑69 (MQ=255)
                                                     tGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAg           >  1:597415/1‑68 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:1498668/68‑1 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:2649669/68‑1 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:1111145/68‑1 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:1865540/68‑1 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:3225549/68‑1 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:3182868/68‑1 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:3120847/68‑1 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:288074/68‑1 (MQ=255)
                                                       tttCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGAt         <  1:285296/68‑1 (MQ=255)
                                                         tCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTa              <  1:1170399/61‑1 (MQ=255)
                                                             cgcAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGt   <  1:2464818/68‑1 (MQ=255)
                                                             cgcAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGt   <  1:2597039/68‑1 (MQ=255)
                                                             cgcAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGt   <  1:2690853/68‑1 (MQ=255)
                                                             cgcAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTa  <  1:3298534/69‑1 (MQ=255)
                                                             cgcAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTa  <  1:3069320/69‑1 (MQ=255)
                                                             cgcAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTa  <  1:2406134/69‑1 (MQ=255)
                                                               |                                                                  
CCACCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTA  >  minE/683624‑683753

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: ‑

GATK/CNVnator alignment

N/A