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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,211,247 A→T 20.2% A35A (GCT→GCA)  cspC ← stress protein, member of the CspA‑family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,211,2470AT20.2% 221.4 / 50.9 100A35A (GCT→GCA) cspCstress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand):  ref base A (30/47);  new base T (10/10);  total (42/58)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

Only 100 of 102 total aligned reads displayed.

CTGGCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTC  >  minE/1211178‑1211315
                                                                     |                                                                    
cTGGCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATa                                                                      <  1:725742/70‑1 (MQ=255)
cTGGCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATa                                                                      <  1:3792426/70‑1 (MQ=255)
   gCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGc                                                                    <  1:3019907/69‑1 (MQ=255)
   gCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCg                                                                   <  1:2478583/70‑1 (MQ=255)
      gTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGgag                                                                >  1:1478149/1‑70 (MQ=255)
          gtgaTTTCGAACTCTACGCGCTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAgtg                                                           <  1:477945/68‑1 (MQ=255)
             aTTTCGAACTCTACGCGCTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTAc                                                        >  1:1059989/1‑71 (MQ=255)
               ttCGAACTCTACGCGCTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTa                                                         <  1:706655/68‑1 (MQ=255)
                tCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGaa                                                              >  1:156016/1‑62 (MQ=255)
                tCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGaa                                                              >  1:2571572/1‑62 (MQ=255)
                tCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGa                                                      <  1:176980/70‑1 (MQ=255)
                 cGAACTCTACGCGCTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGaa                                                     >  1:1637821/1‑70 (MQ=255)
                  gAACTCTACGCGCTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAac                                                    <  1:1652031/70‑1 (MQ=255)
                   aaCTCTACGCGCTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAacac                                                  >  1:372179/1‑71 (MQ=255)
                   aaCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAacac                                                  <  1:24290/71‑1 (MQ=255)
                   aaCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAaca                                                   >  1:2495753/1‑70 (MQ=255)
                    aCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAacac                                                  <  1:3755859/70‑1 (MQ=255)
                    aCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAAcaca                                                 >  1:2657771/1‑71 (MQ=255)
                    aCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAAcaca                                                 >  1:3192446/1‑71 (MQ=255)
                     cTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCg                                                                   <  1:933161/52‑1 (MQ=255)
                     cTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAAcaca                                                 >  1:3527977/1‑70 (MQ=255)
                      tCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGaa                                                              <  1:605378/56‑1 (MQ=255)
                        aaCGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGTAGAAGTGTACGAACACATCt                                              <  1:2715024/70‑1 (MQ=255)
                        aaCGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                             >  1:3407707/1‑71 (MQ=255)
                        aaCGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGAGTACGAACACATCt                                              >  1:103504/1‑70 (MQ=255)
                         aCGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAGGTGTACGAACACATCttt                                            <  1:947240/71‑1 (MQ=255)
                          cGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACTCATCTTtg                                           >  1:1761059/1‑71 (MQ=255)
                          cGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtg                                           >  1:3923645/1‑71 (MQ=255)
                           tttCTGACCTTCGTCCAGAGATTTGTAACCATCGTTCTGGATAGCAGAGAAGTGTa                                                         <  1:2721220/55‑1 (MQ=255)
                           gTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgc                                          >  1:637407/1‑71 (MQ=255)
                            ttCTGACCTTCGTCCAGAGATTTGTAACCATCGTTCTGGATAGCAGAGAAGTGTACGAacactga                                               <  1:621917/65‑4 (MQ=255)
                            ttCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCg                                                                   <  1:2999891/45‑1 (MQ=255)
                            ttCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCg                                                                   <  1:1548692/45‑1 (MQ=255)
                            ttCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCg                                                                   <  1:1544182/45‑1 (MQ=255)
                              cTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgctg                                        <  1:1901325/70‑1 (MQ=255)
                               tGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACAt                                                >  1:2409280/1‑61 (MQ=255)
                                gACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCa                                     >  1:582459/1‑71 (MQ=255)
                                 aCCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCa                                     <  1:543206/70‑1 (MQ=255)
                                 aCCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGcc                                      <  1:1559666/69‑1 (MQ=25)
                                  ccTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCAt                                    >  1:3633317/1‑70 (MQ=255)
                                   cTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGaa                                                     <  1:3806519/52‑1 (MQ=255)
                                   cTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCAt                                    >  1:1249309/1‑69 (MQ=255)
                                     tCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAaca                                                   >  1:223531/1‑52 (MQ=255)
                                     tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAac                                                    >  1:111609/1‑51 (MQ=255)
                                     tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGcc                                      >  1:440163/1‑65 (MQ=19)
                                     tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTcttc                                >  1:3353712/1‑68 (MQ=16)
                                       aGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCg                              >  1:2785260/1‑71 (MQ=255)
                                       aGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCg                              <  1:1982487/71‑1 (MQ=255)
                                       aGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCg                              <  1:77269/71‑1 (MQ=255)
                                        gCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCgg                             <  1:1518876/71‑1 (MQ=255)
                                         ccAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGa                            <  1:559992/71‑1 (MQ=255)
                                         ccAGAGATTTGTAACCATCGTTCTGGATAGCAGAGAAGTGTACGAacact                                                 <  1:2276615/50‑2 (MQ=255)
                                         ccAGAGATTTGTAACCATCGTTCTGGATAGCAGAGAAGTGTACGAacact                                                 <  1:3563071/50‑2 (MQ=255)
                                           agagTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAg                           >  1:1540361/1‑70 (MQ=255)
                                           agagTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGt                          <  1:2122453/71‑1 (MQ=255)
                                             agTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTaa                        >  1:629527/1‑71 (MQ=255)
                                             agTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTaa                        >  1:2564493/1‑71 (MQ=255)
                                               ttttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATg                      <  1:1300803/71‑1 (MQ=255)
                                                 ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATg                      >  1:689997/1‑69 (MQ=255)
                                                 ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATg                      >  1:3587239/1‑69 (MQ=255)
                                                 ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGa                     <  1:3211159/70‑1 (MQ=255)
                                                   gAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAg                   <  1:2114138/70‑1 (MQ=255)
                                                    aaaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAAcc                 <  1:647470/68‑1 (MQ=12)
                                                     aaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTc                                               <  1:1407624/38‑1 (MQ=16)
                                                     aaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTc                                               <  1:103943/38‑1 (MQ=16)
                                                     aaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTtgctg                                        >  1:2345410/3‑47 (MQ=255)
                                                     aaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAAccg                <  1:737923/69‑2 (MQ=255)
                                                     aGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCGGCCGGAGTAATGAAGcc                 >  1:2443707/1‑70 (MQ=255)
                                                     aGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGcc                 >  1:217784/1‑70 (MQ=255)
                                                      gCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                             <  1:2521295/41‑1 (MQ=255)
                                                      gCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGt                          <  1:3169696/60‑1 (MQ=255)
                                                      accATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTct                                  >  1:3407354/2‑51 (MQ=255)
                                                       ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa              <  1:2626606/71‑1 (MQ=255)
                                                        cATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgct                                         >  1:1345245/1‑43 (MQ=255)
                                                        cATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgct                                         >  1:486188/1‑43 (MQ=255)
                                                        cATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa              <  1:247712/70‑1 (MQ=255)
                                                          ttACCCTGGATAGCGGAGAAGTGTACGATCACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaa               <  1:2296236/67‑1 (MQ=255)
                                                          ttACCCTGGATAGCGGAGAAGTGTACGAACACATCt                                              <  1:3368449/36‑1 (MQ=255)
                                                          ttACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCa                                     <  1:591721/45‑1 (MQ=255)
                                                            aCCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgct                                         <  1:1464705/39‑1 (MQ=255)
                                                            aCCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgct                                         <  1:1899480/39‑1 (MQ=255)
                                                            aCCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATc                                   >  1:1419261/1‑45 (MQ=255)
                                                            aCCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCt          <  1:3298623/70‑1 (MQ=255)
                                                             cccTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt         <  1:1499862/70‑1 (MQ=255)
                                                              ccTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa       <  1:1762428/71‑1 (MQ=255)
                                                               cTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtttg       >  1:3132258/1‑69 (MQ=255)
                                                               cTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAg                                 <  1:3017016/44‑1 (MQ=255)
                                                                tGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt         <  1:1583846/67‑1 (MQ=255)
                                                                tGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGc                  >  1:525164/1‑58 (MQ=12)
                                                                tGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCttt        <  1:3433160/68‑1 (MQ=12)
                                                                tGGATAGCGGAGAAGTGTACGAACACATCTTTTCTGCCATCAGCCGGAGTAATGAAGCCaaa              <  1:70980/62‑1 (MQ=255)
                                                                tGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATg                      <  1:3924194/54‑1 (MQ=255)
                                                                 ggATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa              <  1:3065592/61‑1 (MQ=255)
                                                                  gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtttgg      <  1:3510652/68‑3 (MQ=255)
                                                                  gATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGAc    <  1:2987128/70‑1 (MQ=255)
                                                                  gATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGAc    <  1:831281/70‑1 (MQ=255)
                                                                  gATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGACGGAGTAATGAAGCCAAAACCTTTAGAc    <  1:3585649/70‑1 (MQ=255)
                                                                  gATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGACGGAGTAATGAAGCCAAAACCTTTAGAc    <  1:3581191/70‑1 (MQ=255)
                                                                   aTAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTc  >  1:1876307/1‑71 (MQ=255)
                                                                   aTAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTc  >  1:855873/1‑71 (MQ=255)
                                                                     |                                                                    
CTGGCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTC  >  minE/1211178‑1211315

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A