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
A4 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,944,115 A→G noncoding (412/2904 nt) rrlC → 23S ribosomal RNA of rrnC operon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,944,1150AG100.0% 81.5 / NA 29noncoding (412/2904 nt)rrlC23S ribosomal RNA of rrnC operon
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (17/12);  total (17/12)

TGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGG  >  NC_000913/3943993‑3944198
                                                                                                                          |                                                                                   
tgtTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTa                                                                     >  1:571899/1‑139 (MQ=21)
      tGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAgg                                                                        >  1:1032400/1‑130 (MQ=25)
      tGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAgg                                                                        <  2:1032400/130‑1 (MQ=25)
        gAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTcc                                                             >  2:211725/1‑139 (MQ=37)
        gAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTcc                                                             >  1:1507238/1‑139 (MQ=37)
          aGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCa                                                                                  <  1:541901/116‑1 (MQ=25)
          aGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCa                                                                                  >  2:541901/1‑116 (MQ=37)
          aGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCctg                                                           >  1:864845/1‑139 (MQ=37)
          aGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCctg                                                           >  1:894811/1‑139 (MQ=21)
          aGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCctg                                                           >  2:265853/1‑139 (MQ=37)
                tGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCtgactgac                                                     <  1:413611/139‑1 (MQ=25)
                 ggAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGAcc                                                    <  2:894811/139‑1 (MQ=37)
                      ggCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAg                                               <  1:265853/139‑1 (MQ=21)
                           gcgATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAAc                                          <  2:571899/139‑1 (MQ=21)
                                       gACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAg                              >  2:793714/1‑139 (MQ=37)
                                         cAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGcc                                                                                   >  1:1475655/1‑84 (MQ=255)
                                         cAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGt                                 <  1:372307/134‑1 (MQ=21)
                                         cAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGt                                 >  2:372307/1‑134 (MQ=25)
                                         cAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAggg                            >  1:629189/1‑139 (MQ=25)
                                         cAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAggg                            >  2:1347499/1‑139 (MQ=21)
                                              ccGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAgg                       >  1:405438/1‑139 (MQ=37)
                                               cGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGc                      >  2:1657014/1‑139 (MQ=25)
                                                gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTaa                                                                    >  1:1189983/1‑92 (MQ=255)
                                                gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTaa                                                                    <  2:1189983/92‑1 (MQ=37)
                                                         aaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAAcc            <  1:793714/139‑1 (MQ=21)
                                                           tGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTAAGGGAAAGGAGAAAAGAAcccc          >  1:1268165/1‑139 (MQ=255)
                                                                 tatTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAg    <  1:211725/139‑1 (MQ=17)
                                                                 tatTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAg    <  1:1347499/139‑1 (MQ=17)
                                                                   ttGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGGCCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAggg  <  2:864845/139‑1 (MQ=11)
                                                                                                                          |                                                                                   
TGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGG  >  NC_000913/3943993‑3944198

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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