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 1,939,711 A→T 30.5% I127I (ATT→ATA)  ygfX ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,939,7110AT30.5% 130.8 / 72.7 108I127I (ATT→ATA) ygfXhypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (53/22);  new base T (11/22);  total (64/44)
Fisher's exact test for biased strand distribution p-value = 5.45e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 110 total aligned reads displayed.

CTCACTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTT  >  minE/1939646‑1939779
                                                                 |                                                                    
ctcACTGACGGCTTAGCGCAGATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATc                                                                   >  1:1980827/1‑69 (MQ=255)
   aCTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATccgc                                                                >  1:100396/1‑69 (MQ=255)
   aCTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATccgc                                                                >  1:604443/1‑69 (MQ=255)
   aCTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATccgc                                                                >  1:2048598/1‑69 (MQ=255)
   aCTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATccgc                                                                >  1:3105133/1‑69 (MQ=255)
   aCTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATccgc                                                                >  1:2281708/1‑69 (MQ=255)
         ggCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTa                                                            <  1:2380603/67‑1 (MQ=255)
         ggCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTa                                                            <  1:141486/67‑1 (MQ=255)
         ggCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTa                                                            <  1:2255756/67‑1 (MQ=255)
         ggCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTa                                                            <  1:323558/67‑1 (MQ=255)
          gCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTa                                                            <  1:1826024/66‑1 (MQ=255)
                    tatGCTTTGCCGTGATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               <  1:2753490/69‑1 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               >  1:2647298/1‑69 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               <  1:1016681/69‑1 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               <  1:2674249/69‑1 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               >  1:227992/1‑69 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               >  1:2052213/1‑69 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               >  1:2849349/1‑69 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               >  1:3402190/1‑69 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               >  1:1932580/1‑69 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               <  1:1705593/69‑1 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               >  1:1361951/1‑69 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               >  1:1430086/1‑69 (MQ=255)
                    tatGCTTTGCCGTCATCTTTATCTTTGAGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                               <  1:1548297/69‑1 (MQ=255)
                      tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                             >  1:107032/1‑69 (MQ=255)
                      tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                             >  1:1603302/1‑69 (MQ=255)
                      tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                             >  1:759872/1‑69 (MQ=255)
                      tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                             >  1:1026380/1‑69 (MQ=255)
                      tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                             >  1:3414267/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAATAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:1058813/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGc                                            >  1:1968058/1‑68 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:1741053/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:3123728/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:3389589/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:2186296/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:21271/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:3414732/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:1491724/1‑69 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                            <  1:2900586/68‑1 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                            <  1:3268595/68‑1 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                            <  1:2166002/68‑1 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                            <  1:1372495/68‑1 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                            <  1:2065872/68‑1 (MQ=255)
                        cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                            <  1:1936284/68‑1 (MQ=255)
                        cTTTCCCGTCATCTCTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                           >  1:1743491/1‑69 (MQ=255)
                              cGTCATCTTTATCTTTGCGTCTCTTGTTTCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTc                                      <  1:1995561/68‑1 (MQ=255)
                              cGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTc                                      <  1:2652274/68‑1 (MQ=255)
                               gTCATCTTTATCTTTGCGTCTCTTGTTTCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCa                                    >  1:3140356/1‑69 (MQ=255)
                               gTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTcc                                     >  1:611001/1‑68 (MQ=255)
                               gTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCa                                    >  1:2792661/1‑69 (MQ=255)
                               gTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCa                                    >  1:2442512/1‑69 (MQ=255)
                               gTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCa                                    >  1:2044772/1‑69 (MQ=255)
                                tCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCACGCCATTc                                               <  1:2321523/57‑1 (MQ=255)
                                  atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGt                                                             >  1:2861087/1‑41 (MQ=255)
                                  atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                 >  1:3358323/1‑69 (MQ=255)
                                  atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                 >  1:1062398/1‑69 (MQ=255)
                                  atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                 >  1:383169/1‑69 (MQ=255)
                                  atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                 >  1:1814961/1‑69 (MQ=255)
                                  atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                 >  1:1872775/1‑69 (MQ=255)
                                  atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                 >  1:496198/1‑69 (MQ=255)
                                     tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                              >  1:2107925/1‑69 (MQ=255)
                                     tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                              >  1:2394858/1‑69 (MQ=255)
                                     tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                              >  1:2272006/1‑69 (MQ=255)
                                     tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                              >  1:1117295/1‑69 (MQ=255)
                                     tttatctttGCGTCTCTTGTT‑CAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTc                             >  1:1777330/1‑69 (MQ=255)
                                                 tctcTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagc                   >  1:2734350/1‑68 (MQ=255)
                                                 tctcTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagc                   >  1:934226/1‑68 (MQ=255)
                                                   tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                 >  1:532068/1‑68 (MQ=255)
                                                   tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                 >  1:3426486/1‑68 (MQ=255)
                                                   tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                 >  1:249123/1‑68 (MQ=255)
                                                   tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                 >  1:2736027/1‑68 (MQ=255)
                                                   tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                 >  1:1785634/1‑68 (MQ=255)
                                                   tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                 >  1:2686575/1‑68 (MQ=255)
                                                   tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                 >  1:196495/1‑68 (MQ=255)
                                                    ctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCt                                           >  1:1227688/1‑41 (MQ=255)
                                                    ctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTc                                         >  1:970265/1‑43 (MQ=255)
                                                    ctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTc                                         >  1:1140517/1‑43 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:1352534/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:1793089/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:1891364/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:533423/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:1540374/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:524386/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:447577/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:1979503/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:2025229/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:2155303/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:2811412/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:3284130/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:2360822/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:1202710/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:3217365/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:1063873/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:3046285/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:299199/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:2946359/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:1084499/66‑1 (MQ=255)
                                                          gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGGCCATGCTGTCAGCTGCCAGCCATAAATGt          <  1:234714/66‑1 (MQ=255)
                                                                 aaTCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGttt  <  1:2033137/69‑1 (MQ=255)
                                                                 aaTCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGttt  <  1:175261/69‑1 (MQ=255)
                                                                 |                                                                    
CTCACTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTT  >  minE/1939646‑1939779

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