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 F1 I2 R1 758 59.3 2864096 93.9% 2689386 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,994,415 G→A pseudogene (34/60 nt) pbl → pseudogene, peptidoglycan‑binding enzyme family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,994,4150GA100.0% 206.9 / NA 65pseudogene (34/60 nt)pblpseudogene, peptidoglycan‑binding enzyme family
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (32/33);  total (32/33)

CAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTCTA  >  NC_000913/2994311‑2994547
                                                                                                        |                                                                                                                                    
cAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAg                                                                                                    >  2:383001/1‑139 (MQ=255)
     ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  1:635347/139‑1 (MQ=255)
     ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  1:1167584/139‑1 (MQ=255)
     ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  1:1258420/139‑1 (MQ=255)
     ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  1:383001/139‑1 (MQ=255)
              ttATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACa                                                                                                                                   >  1:29481/1‑94 (MQ=255)
              ttATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACa                                                                                                                                   <  2:29481/94‑1 (MQ=255)
                      cGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  2:340907/122‑1 (MQ=255)
                      cGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               >  1:340907/1‑122 (MQ=255)
                        ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATGTTATATACCGGGCTTAATGCACTAAACAAGCGTCAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAATGaaaa                                                                            >  2:918952/1‑139 (MQ=255)
                          ttttGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAaca                                                                          <  2:697465/139‑1 (MQ=255)
                                  tGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACg                                                                  >  1:414791/1‑139 (MQ=255)
                                   ggATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  2:652793/109‑1 (MQ=255)
                                   ggATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               >  1:652793/1‑109 (MQ=255)
                                              aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGtttt                                                      >  2:209309/1‑139 (MQ=255)
                                                    gaCAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACAccc                                                                       >  1:466058/1‑116 (MQ=255)
                                                    gaCAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACAccc                                                                       <  2:466058/116‑1 (MQ=255)
                                                       aGCTATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                     >  2:636587/1‑99 (MQ=255)
                                                       aGCTATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                     <  1:636587/99‑1 (MQ=255)
                                                           atatGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                         <  1:209309/139‑1 (MQ=255)
                                                           atatGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                         <  1:75609/139‑1 (MQ=255)
                                                                          tatatTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  1:1386515/70‑1 (MQ=255)
                                                                          tatatTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCCTCAGCAAAATGAGTCTAAAGCctct                                                                                               >  2:1386515/1‑70 (MQ=255)
                                                                               tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               >  1:420438/1‑65 (MQ=255)
                                                                               tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  2:420438/65‑1 (MQ=255)
                                                                               tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACtgt                                  <  1:715081/126‑1 (MQ=255)
                                                                               tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACtgt                                  >  2:715081/1‑126 (MQ=255)
                                                                                 tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               >  1:583526/1‑63 (MQ=255)
                                                                                 tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  2:583526/63‑1 (MQ=255)
                                                                                   tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAg                                                             <  1:192092/95‑1 (MQ=255)
                                                                                   tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAg                                                             >  2:192092/1‑95 (MQ=255)
                                                                                    ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                            >  1:1055893/1‑79 (MQ=255)
                                                                                    ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                            <  2:1055893/79‑1 (MQ=255)
                                                                                    ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCa                >  1:232687/1‑139 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               >  1:557267/1‑58 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  2:557267/58‑1 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCa                                                                              >  2:1155560/1‑75 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCa                                                                              <  1:1155560/75‑1 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATg              >  2:91684/1‑139 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATg              >  2:595892/1‑139 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATg              >  2:214164/1‑139 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCaa                                                >  2:507231/1‑104 (MQ=255)
                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCaa                                                <  1:507231/104‑1 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAAt                                                                                                              >  1:810167/1‑38 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAAt                                                                                                              <  2:810167/38‑1 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               <  2:285990/53‑1 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                               >  1:285990/1‑53 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCttt                                                                                             <  1:477888/55‑1 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCttt                                                                                             >  2:477888/1‑55 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaa                                                                             >  2:1232663/1‑71 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaa                                                                             <  1:1232663/71‑1 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGa                                >  1:793067/1‑116 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGa                                <  2:793067/116‑1 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt         >  2:276723/1‑139 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt         >  1:807747/1‑139 (MQ=255)
                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt         <  1:91684/139‑1 (MQ=255)
                                                                                             ttAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGa       >  2:85912/1‑139 (MQ=255)
                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                   <  1:1007664/125‑1 (MQ=255)
                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                   >  2:1007664/1‑125 (MQ=255)
                                                                                                aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAttt                     >  2:721474/1‑122 (MQ=255)
                                                                                                aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAttt                     <  1:721474/122‑1 (MQ=255)
                                                                                                  gAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTCTa  <  1:214164/139‑1 (MQ=255)
                                                                                                  gAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTCTa  <  1:85912/139‑1 (MQ=255)
                                                                                                     cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACAccc                                                                       <  2:1280938/67‑1 (MQ=255)
                                                                                                     cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGACTCTTTTTTTTATATAGTGCAAACAccc                                                                       <  1:887027/67‑1 (MQ=255)
                                                                                                        |                                                                                                                                    
CAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTCTA  >  NC_000913/2994311‑2994547

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A