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
A7 F48 I1 R1 508 125.6 4303852 99.2% 4269421 139.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,896,462 C→A D32Y (GAT→TAT)  ygcR ← putative flavoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,896,4620CA98.0% 143.3 / NA 49D32Y (GAT→TAT) ygcRputative flavoprotein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (31/17);  total (31/18)
Fisher's exact test for biased strand distribution p-value = 3.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATCCGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCCCGCCGCCACCAGCGGGAGGGC  >  NC_000913/2896327‑2896595
                                                                                                                                       |                                                                                                                                      
gCCAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGt                                                                                                                                    >  2:702314/1‑140 (MQ=255)
 ccAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCCGTAGCGAAATATACGGTc                                                                                                                                   <  1:1400178/140‑1 (MQ=255)
 ccAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTc                                                                                                                                   <  2:1026013/140‑1 (MQ=255)
 ccAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTc                                                                                                                                   <  1:922925/140‑1 (MQ=255)
 ccAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTc                                                                                                                                   <  1:702314/140‑1 (MQ=255)
 ccAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTc                                                                                                                                   <  2:783728/140‑1 (MQ=255)
 ccAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTc                                                                                                                                   >  2:309850/1‑140 (MQ=255)
     tGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCt                                                                                                                               >  2:823658/1‑140 (MQ=255)
      gCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTATTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCtt                                                                                                                              <  2:1710123/140‑1 (MQ=255)
               gTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGa                                                                                                                    >  1:1737392/1‑140 (MQ=255)
                          aTGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTg                                                                                                         >  2:566960/1‑140 (MQ=255)
                           tGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGc                                                                                                        >  2:453689/1‑140 (MQ=255)
                              tCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCAc                                                                                                     >  2:328399/1‑140 (MQ=255)
                                aaCGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCActc                                                                                                   >  1:1010909/1‑140 (MQ=255)
                                  cgcgGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCATCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCtt                                                                                                 >  2:690637/1‑140 (MQ=255)
                                  cgcgGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCtt                                                                                                 >  1:1072431/1‑140 (MQ=255)
                                         aaaGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGc                                                                                          <  1:566960/140‑1 (MQ=255)
                                                      tACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCa                                                                             <  1:453689/140‑1 (MQ=255)
                                                       aCCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCAt                                                                            >  2:1220463/1‑140 (MQ=255)
                                                         cGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATcc                                                                          >  2:293058/1‑140 (MQ=255)
                                                             tttcCTCTGCGCCAACAGAAGCGGGGCAGCGGCTTGTTCATCAGCCCCGATTAAACTGCGCAGTAGCGAAATTTACGGCCCTCTTTTCCCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGtt                                                                      <  2:655884/140‑1 (MQ=255)
                                                              tttCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATCCGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTc                                                                     <  1:1856488/140‑1 (MQ=255)
                                                                     gcgcCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTa                                                              <  1:293058/140‑1 (MQ=255)
                                                                              gcagcGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAAc                                                     <  1:1128323/140‑1 (MQ=255)
                                                                               cagcGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACa                                                    <  1:1504937/140‑1 (MQ=255)
                                                                                  cgcgGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGaa                                                 >  2:94687/1‑140 (MQ=255)
                                                                                  cgcgGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGaa                                                 >  2:213486/1‑140 (MQ=255)
                                                                                  cgcgGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGaa                                                 >  2:1141544/1‑140 (MQ=255)
                                                                                  cgcgGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGaa                                                 <  1:690637/140‑1 (MQ=255)
                                                                                   gcgGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAAt                                                >  2:1634023/1‑140 (MQ=255)
                                                                                       cAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTc                                            >  2:556248/1‑140 (MQ=255)
                                                                                       cAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTc                                            >  1:2029854/1‑140 (MQ=255)
                                                                                       cAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTc                                            >  2:1667022/1‑140 (MQ=255)
                                                                                       cAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTc                                            >  1:641828/1‑140 (MQ=255)
                                                                                         gCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCAt                                          >  1:1038520/1‑140 (MQ=255)
                                                                                            gCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTCCCC‑GGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCg                                       <  1:309850/140‑1 (MQ=255)
                                                                                             ccggtccatcaGCCCCGATAAACCTTCGCAGTAGCAAAATATACGGTCAGTTTTTACCC‑GGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGc                                      <  2:753745/134‑1 (MQ=255)
                                                                                             ccTGTTCATCAGCCCCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGc                                      <  1:213486/140‑1 (MQ=255)
                                                                                             ccTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGc                                      <  1:556248/140‑1 (MQ=255)
                                                                                             ccTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGACCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGc                                      <  1:94687/140‑1 (MQ=255)
                                                                                              cTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCa                                     <  1:1634023/140‑1 (MQ=255)
                                                                                                    atcaGCACCGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCAcctcct                               >  1:56894/1‑140 (MQ=255)
                                                                                                           ccGAGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTc                        >  1:1180354/1‑140 (MQ=255)
                                                                                                             aaGTAACCTTCACAGCAGGAAAATACACGG‑CCGGTTTTGCCCGTAACCCCCCGCCTGCCGCTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTccc                      <  2:1413054/139‑1 (MQ=255)
                                                                                                              aGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCccg                     >  2:1176347/1‑140 (MQ=255)
                                                                                                              aGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCccg                     >  2:1164436/1‑140 (MQ=255)
                                                                                                              aGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCccg                     >  1:1752129/1‑140 (MQ=255)
                                                                                                              aGTAAACTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCccg                     >  1:1049028/1‑140 (MQ=255)
                                                                                                                   aCTTCGCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCTGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCCCgccgcc                >  1:1421967/1‑140 (MQ=255)
                                                                                                                        gCAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCCCGCCGCCACCAg           >  1:1170749/1‑140 (MQ=255)
                                                                                                                        gCAGTAGCAAAATATCCGTTCCTTTTTTCCCC‑GGCGCCCCCCCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCCCGCCGCCACCAg           <  2:56894/140‑1 (MQ=255)
                                                                                                                         cAGTAGCGAAATATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCCCGCCGCCACCAGc          >  1:1918333/1‑140 (MQ=255)
                                                                                                                           gtgtgaaaaTATACGGTCCGTTTTTCCCC‑AAACCCGCAGCCTCCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTAAATCCTCCTACATTTCCCGCCGCCACCAGCgg        <  2:1421967/134‑1 (MQ=255)
                                                                                                                           atgaaaaaaTATCGGGTCCTTTTTTCCCA‑GGACCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCCCGCCGCCACCAGCgg        <  2:2029854/134‑1 (MQ=255)
                                                                                                                             aGCAAAATATCGGGTCCGCTTTTCCCC‑AGAGCCCCCCCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCCCCTCCTACATTTCCCGCCGCCACCAGCGGGa      <  2:2051731/140‑1 (MQ=255)
                                                                                                                               aaaaaTATCGGGCCCTTTTTCCCCC‑AGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACGGAATGTTCATTCGCACCTCCTACATTTCCCGCCGCCACCAGCGGGAgg    <  2:121565/138‑1 (MQ=255)
                                                                                                                                 aaaTATACGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCCCGCCGCCACCAGCGGGAGGGc  >  2:443047/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                      
GCCAGTGCAATGCCCGTTCATCCCCCATGCTCAACGCGGTTAAAGACATCGGCGTACCGTTTTTTCTCTGCGCCAACAGCAGCGCGGCAGCGGCCTGTTCATCAGCACCGAGTAAACTTCGCAGTAGCGAAATATCCGGTCCGCTTTTACCC‑TGAGCCGCCGCCTGCCACTCTTTTTCCGCCAGCATTCCGGCATCCGGTTCGGCTTTAAACGCTAACAGAATGTTCATTCGCACCTCCTACATTTCCCGCCGCCACCAGCGGGAGGGC  >  NC_000913/2896327‑2896595

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A