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
A3 F1 I1 R1 781 46.9 2231650 93.5% 2086592 109.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,434,929 C→T A236A (GCG→GCA)  truA ← tRNA pseudouridine(38‑40) synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,434,9290CT100.0% 173.5 / NA 54A236A (GCG→GCA) truAtRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/24);  total (30/24)

GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAAT  >  NC_000913/2434823‑2435057
                                                                                                          |                                                                                                                                
gTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAActc                                                                                                  >  2:521032/1‑139 (MQ=255)
  tAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTg                                                                                                <  1:521032/139‑1 (MQ=255)
     tCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTa                                                                                             >  2:170039/1‑139 (MQ=255)
     tCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTa                                                                                             >  1:370438/1‑139 (MQ=255)
                       cccATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGtt                                                                                                                         <  2:912361/93‑1 (MQ=255)
                       cccATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGtt                                                                                                                         >  2:292039/1‑93 (MQ=255)
                       cccATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGtt                                                                                                                         >  1:912361/1‑93 (MQ=255)
                       cccATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGtt                                                                                                                         <  1:292039/93‑1 (MQ=255)
                                    ttGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGAc                                                              >  2:1054302/1‑139 (MQ=255)
                                               tACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGc                                                   >  1:77910/1‑139 (MQ=255)
                                                   ggTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGcc                                               <  2:674412/139‑1 (MQ=255)
                                                    gTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCaa                                                                                                     >  2:87170/1‑84 (MQ=255)
                                                    gTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCaa                                                                                                     <  1:87170/84‑1 (MQ=255)
                                                    gTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCg                                              >  1:1086346/1‑139 (MQ=255)
                                                     tCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGa                                             >  2:320771/1‑139 (MQ=255)
                                                     tCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGa                                             <  2:370438/139‑1 (MQ=255)
                                                     tCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGa                                             >  1:733360/1‑139 (MQ=255)
                                                     tCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGa                                             >  1:889056/1‑139 (MQ=255)
                                                              tCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCaa                                                                                                     <  2:510135/74‑1 (MQ=255)
                                                              tCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCaa                                                                                                     >  1:510135/1‑74 (MQ=255)
                                                              tCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAgg                                                    >  2:735606/1‑123 (MQ=255)
                                                              tCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAgg                                                    <  1:735606/123‑1 (MQ=255)
                                                              tCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTcc                                    <  1:1054302/139‑1 (MQ=255)
                                                              tCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTcc                                    <  2:889056/139‑1 (MQ=255)
                                                                   cgcgACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACa                                           <  2:1011971/127‑1 (MQ=255)
                                                                   cgcgACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACa                                           >  1:1011971/1‑127 (MQ=255)
                                                                   cgcgACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg                                  <  2:1102498/136‑1 (MQ=255)
                                                                   cgcgACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg                                  >  1:1102498/1‑136 (MQ=255)
                                                                   cgcgACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc                               >  1:217830/1‑139 (MQ=255)
                                                                   cgcgACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc                               >  2:902783/1‑139 (MQ=255)
                                                                   cgcgACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc                               >  2:182253/1‑139 (MQ=255)
                                                                      gACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCata                            <  1:249384/139‑1 (MQ=255)
                                                                        ccAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATatg                          <  2:217830/139‑1 (MQ=255)
                                                                             tACAGCCCTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTa                     <  1:938589/139‑1 (MQ=255)
                                                                                  cccTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCa                                                                                                      <  2:28833/53‑1 (MQ=255)
                                                                                  cccTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCa                                                                                                      >  1:28833/1‑53 (MQ=255)
                                                                                  cccTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACaaaa                >  2:354727/1‑139 (MQ=255)
                                                                                  cccTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACaaaa                >  2:446510/1‑139 (MQ=255)
                                                                                  cccTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACa                   >  1:472460/1‑136 (MQ=255)
                                                                                  cccTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACa                   <  2:472460/136‑1 (MQ=255)
                                                                                    cTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGa                                             >  1:624254/1‑108 (MQ=255)
                                                                                    cTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGa                                             <  2:624254/108‑1 (MQ=255)
                                                                                    cTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc                               <  2:301094/122‑1 (MQ=255)
                                                                                    cTTCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc                               >  1:301094/1‑122 (MQ=255)
                                                                                     ttCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCa             >  2:471138/1‑139 (MQ=255)
                                                                                     ttCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCa             <  1:170039/139‑1 (MQ=255)
                                                                                      tCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCAc                                                                  <  1:656202/85‑1 (MQ=255)
                                                                                      tCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCAt            >  1:715147/1‑139 (MQ=255)
                                                                                      tCCGCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGCCAc                                                                  >  2:656202/1‑85 (MQ=255)
                                                                                         gCTTTTGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCg         <  1:182253/139‑1 (MQ=255)
                                                                                            tttGCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCtt      >  2:51713/1‑139 (MQ=255)
                                                                                               gCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc                               <  1:911574/111‑1 (MQ=255)
                                                                                               gCCGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc                               >  2:911574/1‑111 (MQ=255)
                                                                                                ccGTTGCTGCTGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAat  <  2:589862/139‑1 (MQ=255)
                                                                                                          |                                                                                                                                
GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAAT  >  NC_000913/2434823‑2435057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A