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 581,912 T→C 36.1% F650F (TTT→TTC)  clpA → ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE581,9120TC36.1% 66.2 / 64.6 105F650F (TTT→TTC) clpAATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
Reads supporting (aligned to +/- strand):  ref base T (31/36);  new base C (27/11);  total (58/47)
Fisher's exact test for biased strand distribution p-value = 1.56e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.23e-01

Only 100 of 116 total aligned reads displayed.

CGATGGAAGAGATCAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCAGC  >  minE/581845‑581979
                                                                   |                                                                   
cgatgGAAGAGATCAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTg                                                                    <  1:8112/69‑1 (MQ=255)
cgatgGAAGAGATCAAGAAGATCTTTACACCGGAATTCCGTAACCGGCTCGACAACATTATCTGGTTTg                                                                    <  1:787726/69‑1 (MQ=255)
       agagATCAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCt                                                             >  1:939250/1‑69 (MQ=255)
       agagATCAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCt                                                             >  1:1785079/1‑69 (MQ=255)
          gaTCAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTc                                                          >  1:1470501/1‑69 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:154077/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:2049277/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:2924150/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:1840550/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:3160350/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:3391698/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:1675532/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:636038/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:1549714/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:740120/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:1504249/1‑68 (MQ=255)
             cAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCaa                                                        >  1:905401/1‑68 (MQ=255)
                gaagaTCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCg                                                     <  1:707641/68‑1 (MQ=255)
                gaagaTCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCg                                                     <  1:528601/68‑1 (MQ=255)
                gaagaTCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCg                                                     <  1:2479030/68‑1 (MQ=255)
                         tACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGatc                                                                 <  1:2953861/47‑1 (MQ=255)
                         tACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATcc                                            >  1:2134283/1‑68 (MQ=255)
                         tACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATcc                                            >  1:935780/1‑68 (MQ=255)
                         tACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATcc                                            >  1:1980503/1‑68 (MQ=255)
                         tACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATcc                                            >  1:3177153/1‑68 (MQ=255)
                         tACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATcc                                            >  1:29066/1‑68 (MQ=255)
                         tACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATcc                                            >  1:1273449/1‑68 (MQ=255)
                               ggAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggt                                     <  1:2305010/69‑1 (MQ=255)
                               ggAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggt                                     <  1:1142419/69‑1 (MQ=255)
                               ggAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggt                                     <  1:1120593/69‑1 (MQ=255)
                               ggAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggt                                     <  1:2316497/69‑1 (MQ=255)
                               ggAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggt                                     <  1:1465896/69‑1 (MQ=255)
                               ggAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggt                                     <  1:1469780/69‑1 (MQ=255)
                                gAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggtg                                    <  1:1257363/69‑1 (MQ=255)
                                gAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggtg                                    <  1:2971651/69‑1 (MQ=255)
                                gAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggt                                     <  1:1216790/68‑1 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGatca                                                                >  1:1261885/1‑36 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGgtggtg                                 >  1:2168123/1‑67 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGgtggtg                                 >  1:2435798/1‑67 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGgtggtg                                 >  1:1974224/1‑67 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGgtggtg                                 >  1:3020611/1‑67 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGgtggtg                                 >  1:3294145/1‑67 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGgtggtg                                 >  1:3353400/1‑67 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:2540569/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:374459/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:243823/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:921097/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:97796/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:1709453/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:2231105/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:2226890/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:1728401/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:179256/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:1692083/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:1969942/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:1553086/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:1086994/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGtggtgg                                >  1:1520664/1‑68 (MQ=255)
                                     ccGTAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACAGACGTGATCCATCAGGtggtgg                                >  1:2305291/1‑68 (MQ=255)
                                        tAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATaa                            <  1:2869545/69‑1 (MQ=255)
                                        tAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATaa                            <  1:2173234/69‑1 (MQ=255)
                                        tAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATaa                            <  1:2595846/69‑1 (MQ=255)
                                        tAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATaa                            <  1:1950141/69‑1 (MQ=255)
                                        tAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATaa                            <  1:181444/69‑1 (MQ=255)
                                        tAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATaa                            <  1:77698/69‑1 (MQ=255)
                                        tAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATaa                            <  1:2329556/69‑1 (MQ=255)
                                        tAACCGTCTCGACAACATTATCTGGTTCGATCATCTGTCAACCGACGTGATCCATCAGGT‑GTGGATaa                            <  1:470918/68‑1 (MQ=255)
                                             gTCTCTACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAAtt                         >  1:1745869/1‑67 (MQ=255)
                                             gTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTc                        >  1:1055043/1‑68 (MQ=255)
                                             gTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCa                       >  1:1225632/1‑69 (MQ=255)
                                             gTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCa                       >  1:3318375/1‑69 (MQ=255)
                                             gTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCa                       >  1:2565809/1‑69 (MQ=255)
                                             gTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCa                       >  1:2566727/1‑69 (MQ=255)
                                               ctcGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCAtc                     <  1:3429389/69‑1 (MQ=255)
                                                tcGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAggt                                     <  1:1812564/52‑1 (MQ=255)
                                                tcGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCAtc                     <  1:767963/68‑1 (MQ=255)
                                                    caacaTTATCTGGTTTGATCATCTCTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCAtcgtcg                 <  1:621885/68‑1 (MQ=255)
                                                        aTTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTg            <  1:539764/69‑1 (MQ=255)
                                                        aTTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTg            <  1:1513538/69‑1 (MQ=255)
                                                        aTTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTg            <  1:951459/69‑1 (MQ=255)
                                                        aTTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTg            <  1:3252969/69‑1 (MQ=255)
                                                         ttATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGc           <  1:2818138/69‑1 (MQ=255)
                                                         ttATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGc           <  1:1028324/69‑1 (MQ=255)
                                                         ttATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGc           <  1:2543686/69‑1 (MQ=255)
                                                         ttATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGc           <  1:2624570/69‑1 (MQ=255)
                                                         ttATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGc           <  1:114493/69‑1 (MQ=255)
                                                         ttATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGc           <  1:2630576/69‑1 (MQ=255)
                                                         ttATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGc           <  1:2673696/69‑1 (MQ=255)
                                                         ttATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGc           <  1:2141016/69‑1 (MQ=255)
                                                          tATCTGGTTTGTTCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCAtcgtcg                 <  1:322283/62‑1 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCa    <  1:2866981/67‑1 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCa    <  1:3405849/67‑1 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCa    <  1:1297822/67‑1 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCa    <  1:1921851/67‑1 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCa    <  1:1088077/67‑1 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCa    <  1:261682/67‑1 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCa    <  1:3250736/67‑1 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCAGc  >  1:2951577/1‑69 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCAGc  >  1:3184283/1‑69 (MQ=255)
                                                                  ttGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCAGc  >  1:536762/1‑69 (MQ=255)
                                                                   |                                                                   
CGATGGAAGAGATCAAGAAGATCTTTACACCGGAATTCCGTAACCGTCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATCGTCGAGTTGCAGGTTCAGC  >  minE/581845‑581979

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A