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 769,100 A→T 31.3% I201I (ATT→ATA)  phoP ← DNA‑binding response regulator in two‑component regulatory system with PhoQ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE769,1000AT31.3% 175.2 / 107.0 150I201I (ATT→ATA) phoPDNA‑binding response regulator in two‑component regulatory system with PhoQ
Reads supporting (aligned to +/- strand):  ref base A (36/67);  new base T (13/34);  total (49/101)
Fisher's exact test for biased strand distribution p-value = 4.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

Only 100 of 152 total aligned reads displayed.

AGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCG  >  minE/769033‑769164
                                                                   |                                                                
aGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGaa                                                                 >  1:841645/1‑69 (MQ=255)
aGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGaa                                                                 >  1:3216073/1‑69 (MQ=255)
    cAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAAtttt                                                             >  1:450414/1‑69 (MQ=255)
    cAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAAtttt                                                             >  1:2899487/1‑69 (MQ=255)
            aCAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCa                                                     <  1:2550300/69‑1 (MQ=255)
            aCAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCa                                                     <  1:1914890/69‑1 (MQ=255)
            aCAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCa                                                     <  1:3292267/69‑1 (MQ=255)
                 tAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:2838945/62‑1 (MQ=255)
                 tAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:52336/62‑1 (MQ=255)
                 tAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:3232205/62‑1 (MQ=255)
                 tAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:2373325/62‑1 (MQ=255)
                 tAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:2245461/62‑1 (MQ=255)
                 tAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:1594639/62‑1 (MQ=255)
                  aGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTc                                               <  1:1358350/69‑1 (MQ=255)
                   gCCCTGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTc                                               <  1:1983105/68‑1 (MQ=255)
                   gCCCTGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTc                                               <  1:81381/68‑1 (MQ=255)
                     ccTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTccc                                             >  1:71608/1‑68 (MQ=255)
                     ccTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTccc                                             >  1:1805642/1‑68 (MQ=255)
                     ccTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTccc                                             >  1:3059380/1‑68 (MQ=255)
                     ccTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTccc                                             >  1:617186/1‑68 (MQ=255)
                     ccTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGAAGACGTccc                                             >  1:1673144/1‑68 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:1255141/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:2204395/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:725618/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:901994/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:3037774/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:383309/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:2581996/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:1144749/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:1296311/1‑69 (MQ=255)
                       tGGCCGCGAACGGTGGTAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATc                                          >  1:1284288/1‑69 (MQ=255)
                           cgcgAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:615136/67‑1 (MQ=255)
                           cgcgAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:963873/67‑1 (MQ=255)
                           cgcgAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:738869/67‑1 (MQ=255)
                           cgcgAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:2751953/67‑1 (MQ=255)
                           cgcgAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:2795117/67‑1 (MQ=255)
                           cgcgAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:760302/67‑1 (MQ=255)
                           cgcgAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:3131844/67‑1 (MQ=255)
                                    tggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:1003385/69‑1 (MQ=255)
                                    tggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:2080718/69‑1 (MQ=255)
                                    tggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:398558/69‑1 (MQ=255)
                                    tggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:2632800/69‑1 (MQ=255)
                                    tggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:3025915/69‑1 (MQ=255)
                                    tggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:3336168/69‑1 (MQ=255)
                                    tggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:2515226/69‑1 (MQ=255)
                                     ggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:2569099/68‑1 (MQ=255)
                                     ggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGt                            <  1:3302993/69‑1 (MQ=255)
                                     ggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGt                            <  1:601296/69‑1 (MQ=255)
                                     ggtAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGt                            <  1:1852661/69‑1 (MQ=255)
                                     ggtAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGt                            <  1:2358283/69‑1 (MQ=255)
                                     ggtAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGt                            <  1:2954127/69‑1 (MQ=255)
                                     ggtAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGt                            <  1:1856299/69‑1 (MQ=255)
                                     ggtAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGt                            <  1:1938018/69‑1 (MQ=255)
                                     ggtAATCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGt                            <  1:1932801/69‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:228435/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:115180/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:879067/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:1581640/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:1761211/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:1828664/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:1889842/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:2094254/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:564564/68‑1 (MQ=255)
                                        aaTCACTTCTTGCGGATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCAGTACATCTATGGTAt                          <  1:2611443/68‑1 (MQ=255)
                                         aTCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:2753986/64‑1 (MQ=255)
                                         aTCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:623681/64‑1 (MQ=255)
                                         aTCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:2669333/64‑1 (MQ=255)
                                         aTCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:1317235/64‑1 (MQ=255)
                                           cACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:2007051/36‑1 (MQ=255)
                                           cACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:1520742/36‑1 (MQ=255)
                                           cACTTCTTGGGGATATTGTGCCTGAATTTTTTTgcg                                                       <  1:1454273/36‑1 (MQ=255)
                                            aCTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGc                       >  1:57169/1‑67 (MQ=255)
                                            aCTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCtt                     >  1:1030563/1‑69 (MQ=255)
                                            aCTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCtt                     >  1:3117542/1‑69 (MQ=255)
                                            aCTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCtt                     >  1:2192798/1‑69 (MQ=255)
                                              ttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGCCGt                                                >  1:2615277/1‑40 (MQ=255)
                                              ttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGt                                                >  1:1912938/1‑40 (MQ=255)
                                              ttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGt                                                >  1:265210/1‑40 (MQ=255)
                                              ttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGt                                                >  1:1107893/1‑40 (MQ=255)
                                                 ttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgt                             <  1:2113070/56‑2 (MQ=255)
                                                   ggggATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:1429558/43‑1 (MQ=255)
                                                   ggggATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:2129696/43‑1 (MQ=255)
                                                   ggggATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:622286/43‑1 (MQ=255)
                                                   ggggATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAg                                        <  1:2698657/43‑1 (MQ=255)
                                                      gATATTGTGCCTGTATTTTTTTGCGCAGACGTCCCATCATTACATCTATTGt                            <  1:1380967/52‑1 (MQ=255)
                                                          ttGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGTCTTTCCCGCAGCTCCGc       >  1:3408877/1‑69 (MQ=255)
                                                          ttGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCTCAGCTCCGc       <  1:1646820/69‑1 (MQ=255)
                                                          ttGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGc       >  1:600234/1‑69 (MQ=255)
                                                          ttGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGc       >  1:513557/1‑69 (MQ=255)
                                                          ttGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGc       >  1:2827719/1‑69 (MQ=255)
                                                          ttGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGc       >  1:811889/1‑69 (MQ=255)
                                                            gtgCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:456465/45‑1 (MQ=255)
                                                            gtgCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATgg                             <  1:3087107/45‑1 (MQ=255)
                                                            gtgCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCAt     >  1:843174/1‑69 (MQ=255)
                                                            gtgCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCAt     >  1:109477/1‑69 (MQ=255)
                                                            gtgCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCAt     >  1:2045499/1‑69 (MQ=255)
                                                            gtgCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCAt     >  1:219883/1‑69 (MQ=255)
                                                            gtgCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCAt     >  1:2707670/1‑69 (MQ=255)
                                                               ccTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCg  <  1:2138633/69‑1 (MQ=255)
                                                               ccTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCg  <  1:2150735/69‑1 (MQ=255)
                                                                   |                                                                
AGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCG  >  minE/769033‑769164

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