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
A14 F1 I2 R1 70 59.9 2639336 94.5% 2494172 113.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,806,042 (C)6→7 coding (42/759 nt) ydiY ← acid‑inducible putative outer membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,806,0361.C94.2% 174.3 / 2.5 52coding (48/759 nt)ydiYacid‑inducible putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base . (0/3);  new base C (25/24);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 2.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

CTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑C‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGAAAGG  >  NC_000913/1805905‑1806169
                                                                                                                                    |                                                                                                                                       
cTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑ccccc                                                                                                                                <  1:1082359/139‑2 (MQ=255)
cTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑ccccc                                                                                                                                <  1:135941/139‑2 (MQ=255)
cTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑ccccc                                                                                                                                >  2:1082359/1‑138 (MQ=255)
 ttttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAGACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑ccccc                                                                                                                                <  1:186847/138‑2 (MQ=255)
 ttttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑cccccg                                                                                                                               <  1:564048/139‑3 (MQ=255)
 ttttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑ccccc                                                                                                                                >  2:186847/1‑137 (MQ=255)
  tttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑cccccgc                                                                                                                              <  1:668142/139‑4 (MQ=255)
             cTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑C‑C‑CCCCGCCAACATAACGAt                                                                                                                   <  2:1216998/139‑1 (MQ=255)
                aTTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATgg                                                                                                                 >  2:639813/1‑139 (MQ=255)
                aTTGTGCAAGATATCCTGCATTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATgg                                                                                                                 >  2:17065/1‑139 (MQ=255)
                    tgCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAgg                                                                                                             >  1:1274486/1‑139 (MQ=255)
                    tgCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAgg                                                                                                             >  1:552773/1‑139 (MQ=255)
                    tgCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAgg                                                                                                             >  1:493315/1‑139 (MQ=255)
                      cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           <  1:259885/139‑1 (MQ=255)
                      cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           >  1:686842/1‑139 (MQ=255)
                      cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           <  2:676387/139‑1 (MQ=255)
                              ccTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           >  1:933542/1‑131 (MQ=255)
                              ccTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           <  2:933542/131‑1 (MQ=255)
                              ccTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTc                                                                                                   >  1:1198914/1‑139 (MQ=255)
                                tGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCaa                                                                                                 <  2:686842/139‑1 (MQ=255)
                                   gTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATg                                                                                                                                          <  2:1230832/97‑1 (MQ=255)
                                   gTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATg                                                                                                                                          >  1:1230832/1‑97 (MQ=255)
                                   gTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAg                                                                                              >  2:91261/1‑139 (MQ=255)
                                    ttCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGc                                                                                             >  1:518764/1‑139 (MQ=255)
                                      cAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCtt                                                                                           <  2:1071788/139‑1 (MQ=255)
                                                tCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCaa                                                                                 <  2:552773/139‑1 (MQ=255)
                                                 cGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACg                                                                                                                     >  1:4661/1‑102 (MQ=255)
                                                 cGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACg                                                                                                                     <  2:4661/102‑1 (MQ=255)
                                                  gAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAaga                                                                               <  1:407192/139‑1 (MQ=255)
                                                   aaaGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           <  2:310841/110‑1 (MQ=255)
                                                   aaaGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           >  1:310841/1‑110 (MQ=255)
                                                   aaaGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAagag                                                                              >  1:960360/1‑139 (MQ=255)
                                                          ttttAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTac                                                                       <  2:1198914/139‑1 (MQ=255)
                                                          ttttAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTac                                                                       <  2:365834/139‑1 (MQ=255)
                                                            ttAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTacaa                                                                     <  2:1108281/139‑1 (MQ=255)
                                                               gcgcTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTAcaacaa                                                                  <  1:91261/139‑1 (MQ=255)
                                                                 gcTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACaaaa                                                                >  1:354656/1‑139 (MQ=255)
                                                                      cAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAaga                                                           <  1:550851/139‑1 (MQ=255)
                                                                              tcCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATcg                                                   <  2:1274486/139‑1 (MQ=255)
                                                                               ccATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTac                                                                       <  1:1210382/118‑1 (MQ=255)
                                                                               ccATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTac                                                                       >  2:1210382/1‑118 (MQ=255)
                                                                               ccATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATcgc                                                  >  2:801514/1‑139 (MQ=255)
                                                                                   gACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCtt                                                                                           >  1:322055/1‑94 (MQ=255)
                                                                                   gACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCtt                                                                                           <  2:322055/94‑1 (MQ=255)
                                                                                   gACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTc                                              >  1:546413/1‑139 (MQ=255)
                                                                                     cAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑ccccc                                                                                                                                <  2:402395/54‑2 (MQ=255)
                                                                                     cAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑c‑c‑ccccc                                                                                                                                >  1:402395/1‑53 (MQ=255)
                                                                                        tAAAAACGGTATCATCGGCAGCTGCATTCAGTGACGCAAACAAGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGc                                                                                             <  1:928322/87‑1 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           <  2:1088828/73‑1 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           >  1:1088828/1‑73 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGc                                                                                             >  2:928322/1‑87 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCa                                                                                         <  1:899876/91‑1 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCa                                                                                         >  2:899876/1‑91 (MQ=255)
                                                                                                        ggCAGCTGCATTCAGGGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATc                         <  1:724084/139‑1 (MQ=255)
                                                                                                                 aTTCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAg                <  2:354656/139‑1 (MQ=255)
                                                                                                                 aTTCAGTGACGCAAACATG‑C‑CGCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAg                <  2:420480/139‑1 (MQ=255)
                                                                                                                  ttCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           <  2:424152/47‑1 (MQ=255)
                                                                                                                  ttCAGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGaa                                                                                                           >  1:424152/1‑47 (MQ=255)
                                                                                                                  ctCAGTGACGCAAACATG‑CTC‑CCCCGCCAACATAACGATGGCAGGAACTGGCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGc               <  1:1172978/138‑1 (MQ=255)
                                                                                                                     aGTGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTc            >  1:1053134/1‑139 (MQ=255)
                                                                                                                       tGACGCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTccc          >  1:604433/1‑139 (MQ=255)
                                                                                                                           gCAAACATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGa      <  2:731415/139‑1 (MQ=255)
                                                                                                                               aCATGCC‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGAAAgg  >  1:1038042/1‑139 (MQ=255)
                                                                                                                                    |                                                                                                                                       
CTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑C‑C‑CCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGAAAGG  >  NC_000913/1805905‑1806169

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A