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
A18 F48 I1 R1 70 76.3 2572620 98.7% 2539175 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,140,113 G→T A69D (GCC→GAC)  hybF ← hydrogenase maturation protein HybF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,140,1130GT94.7% 181.8 / 3.4 58A69D (GCC→GAC) hybFhydrogenase maturation protein HybF
Reads supporting (aligned to +/- strand):  ref base G (2/1);  new base T (17/37);  total (20/38)
Fisher's exact test for biased strand distribution p-value = 2.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

TTATTCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGGCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAGCGCGCCAATTTCCAGCCACACGGCGGTGACGC  >  NC_000913/3139977‑3140245
                                                                                                                                        |                                                                                                                                    
ttATTCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCgg                                                                                                                                   <  1:1186510/140‑1 (MQ=255)
ttATTCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCgg                                                                                                                                   >  2:51010/1‑140 (MQ=255)
 tATTCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCggg                                                                                                                                  <  1:840904/140‑1 (MQ=255)
  aTTCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGt                                                                                                                                 >  1:817641/1‑140 (MQ=255)
   ttCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGtt                                                                                                                                >  1:16130/1‑140 (MQ=255)
    tCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGttt                                                                                                                               >  1:1227341/1‑140 (MQ=255)
    tCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGttt                                                                                                                               >  1:545888/1‑140 (MQ=255)
     aaaCTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTta                                                                                                                              <  2:35887/139‑1 (MQ=255)
       aCTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGGCGGGTTtata                                                                                                                            >  1:408929/1‑140 (MQ=255)
         ttCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGa                                                                                                                          >  1:1174424/1‑140 (MQ=255)
          tCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGAc                                                                                                                         <  1:800907/140‑1 (MQ=255)
          tCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGAc                                                                                                                         >  1:411385/1‑140 (MQ=255)
          tCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGAc                                                                                                                         <  2:1102083/140‑1 (MQ=255)
          tCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGAc                                                                                                                         <  2:479507/140‑1 (MQ=255)
          tCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAAACTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGAc                                                                                                                         <  1:490011/140‑1 (MQ=255)
             aTACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGat                                                                                                                      >  1:82195/1‑140 (MQ=255)
               aCTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGatat                                                                                                                    <  2:234737/140‑1 (MQ=255)
                     gACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAAt                                                                                                              >  1:496906/1‑140 (MQ=255)
                         aTCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCa                                                                                                          <  2:491629/140‑1 (MQ=255)
                             gCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACTATATGTAAATCGCACCCt                                                                                                      <  1:840218/140‑1 (MQ=255)
                                 aTCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTgcg                                                                                                  <  1:1132462/140‑1 (MQ=255)
                                 aTCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTgcg                                                                                                  <  1:983592/140‑1 (MQ=255)
                                 aTCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTgcg                                                                                                  <  1:221054/140‑1 (MQ=255)
                                        gTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGt                                                                                           >  2:934367/1‑140 (MQ=255)
                                         tATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGtt                                                                                          <  2:753893/140‑1 (MQ=255)
                                                    aaCCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGAc                                                                               <  2:16130/140‑1 (MQ=255)
                                                         cTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAAttt                                                                          >  1:722872/1‑140 (MQ=255)
                                                          tCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTc                                                                         <  2:411385/140‑1 (MQ=255)
                                                           cGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGTAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCa                                                                        <  2:209819/140‑1 (MQ=255)
                                                            gCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCaa                                                                       <  1:280845/140‑1 (MQ=255)
                                                            gCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCaa                                                                       >  1:1207778/1‑140 (MQ=255)
                                                                  aCAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCaa                                                                       <  2:168807/134‑1 (MQ=255)
                                                                  aCAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCaa                                                                       >  1:168807/1‑134 (MQ=255)
                                                                   cAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCTTTGCGCCACCGTTCCGTGGCAGACAATTTCATAACTaaa                                                                <  1:841386/140‑1 (MQ=255)
                                                                   cAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCTCCACCGTTCCGTGGCAGACAATTTCAAAACTaaa                                                                <  2:1174424/140‑1 (MQ=255)
                                                                      agCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAacg                                                             >  1:811946/1‑140 (MQ=255)
                                                                        cGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAacgga                                                           <  2:119866/140‑1 (MQ=255)
                                                                        cGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGGCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAacgga                                                           >  1:1201700/1‑140 (MQ=255)
                                                                        cGGACACTGAGCATCGTGATGATGAATCTCCACCACCTGGCTGCAATCCCAGCACAAAGCCTGGTCGGGTTTATAAACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAacgga                                                           <  2:1249697/140‑1 (MQ=255)
                                                                             acTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGGCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGgcg                                                      <  2:408929/140‑1 (MQ=255)
                                                                                  gcATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCtctc                                                 <  2:90061/140‑1 (MQ=255)
                                                                                  gcATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCtctc                                                 <  2:1227341/140‑1 (MQ=255)
                                                                                  gcATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCtctc                                                 <  1:934367/140‑1 (MQ=255)
                                                                                  gcATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCtctc                                                 <  2:545888/140‑1 (MQ=255)
                                                                                  gcATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCACACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCtctc                                                 <  2:496906/140‑1 (MQ=255)
                                                                                    aTCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAGGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTctcct                                               <  2:190405/140‑1 (MQ=255)
                                                                                    aTCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTctcct                                               <  1:264962/140‑1 (MQ=255)
                                                                                    aTCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTctcct                                               <  2:705258/140‑1 (MQ=255)
                                                                                    aTCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTctcct                                               <  1:1264240/140‑1 (MQ=255)
                                                                                    aTCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTctcct                                               <  2:1128155/140‑1 (MQ=255)
                                                                                       gTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCaa                                            <  2:902765/140‑1 (MQ=255)
                                                                                              tgaATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGga                                     >  1:584237/1‑140 (MQ=255)
                                                                                                  tctcCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAgc                                 >  2:670757/1‑140 (MQ=255)
                                                                                                              ggCTGCAATCCCAGCACCAAGCCTGGCCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAGCGCGCCAATTTcc                     >  1:738507/1‑140 (MQ=255)
                                                                                                                cTGCAATCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAGCTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAGCGCGCCAATTTCCAg                   <  2:113676/140‑1 (MQ=255)
                                                                                                                     aTCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAGCGCGCCAATTTCCAGCcaca              <  2:235790/140‑1 (MQ=255)
                                                                                                                     aTCCCAGCACCAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAGCGCGCCAATTTCCAGCcaca              <  2:738507/140‑1 (MQ=255)
                                                                                                                               cAAGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAGCGCGCCAATTTCCAGCCACACGGCGGTGAc    <  1:670757/140‑1 (MQ=255)
                                                                                                                                 aGCCTGGTCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAGCGCGCCAATTTCCAGCCACACGGCGGTGAcgc  >  2:724097/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                    
TTATTCAACTTCAATACTTTTGACGATCAGCGAATCGCCGGTATCGACACGCAACCGCTCGCCGTGACAGAGCGGACACTGCGCATCGTGCTGATGAATCTCCACCACCTGGCTGCAATCCCAGCACCAAGCCTGGGCGGGTTTATAGACGATATGTAAATCGCACCCTTGCGCCACCGTTCCGTGGCAGACAATTTCAAAACTAAAACGGACGGCGCTCTCCTCAACGCAGGAGAGCGCGCCAATTTCCAGCCACACGGCGGTGACGC  >  NC_000913/3139977‑3140245

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A