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
A9 F1 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,645,013 C→T *771* (TAG→TAA)  pbpC ← penicillin‑insensitive murein repair transglycosylase, inactive transpeptidase domain protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,645,0130CT100.0% 177.1 / NA 55*771* (TAG→TAA) pbpCpenicillin‑insensitive murein repair transglycosylase, inactive transpeptidase domain protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/29);  total (26/29)

TCTGTTGTTGTCTGTACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCATTCAGA  >  NC_000913/2644884‑2645142
                                                                                                                                 |                                                                                                                                 
tCTGTTGTTGTCTGTACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATg                                                                                                                          <  2:817938/139‑1 (MQ=255)
            tGTACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACt                                                                                                              >  1:342164/1‑139 (MQ=255)
                   gCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGa                                                                                                       >  2:798502/1‑139 (MQ=255)
                   gCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGa                                                                                                       <  1:798502/139‑1 (MQ=255)
                    cGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGAt                                                                                                      >  1:605619/1‑139 (MQ=255)
                    cGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGAt                                                                                                      >  1:26908/1‑139 (MQ=255)
                    cGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGAt                                                                                                      <  2:1253281/139‑1 (MQ=255)
                         gagaTGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGcc                                                                                                 <  2:342164/139‑1 (MQ=255)
                              ggCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACg                                                                                            <  2:26908/139‑1 (MQ=255)
                                   ggATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGccc                                                                                                >  2:855965/1‑130 (MQ=255)
                                   ggATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGccc                                                                                                <  1:855965/130‑1 (MQ=255)
                                    gATTATAATGAGCCACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGCCAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTcatcc                                                                                      <  1:1260935/139‑1 (MQ=255)
                                              aGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCa                                                                                                                <  2:357839/103‑1 (MQ=255)
                                              aGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCa                                                                                                                >  1:357839/1‑103 (MQ=255)
                                               gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCa                                                                                                                            <  2:132094/90‑1 (MQ=255)
                                               gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCa                                                                                                                            >  1:132094/1‑90 (MQ=255)
                                               gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGccc                                                                                                <  2:1022549/118‑1 (MQ=255)
                                               gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGccc                                                                                                >  1:1022549/1‑118 (MQ=255)
                                                cAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCTGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGGCATCCATCACCAGCAAt                                                                          <  1:1051194/139‑1 (MQ=255)
                                                  aCAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTg                                                                        <  2:605619/139‑1 (MQ=255)
                                                   cAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCAcc                                                                                <  2:54328/130‑1 (MQ=255)
                                                   cAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCAcc                                                                                >  1:54328/1‑130 (MQ=255)
                                                   cAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGa                                                                       >  2:884669/1‑139 (MQ=255)
                                                        ccGTTGACTATTGATGAAGGAAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATaagc                                                                  >  1:1078181/1‑137 (MQ=255)
                                                                        aaGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAACCAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCaaa                                                  >  1:1061813/1‑139 (MQ=255)
                                                                          ggTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGt                                                      >  1:1356349/1‑133 (MQ=255)
                                                                          ggTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGt                                                      <  2:1356349/133‑1 (MQ=255)
                                                                                    ttttAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCAcc                                                                                <  2:1579532/97‑1 (MQ=255)
                                                                                    ttttAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCAcc                                                                                >  1:1579532/1‑97 (MQ=255)
                                                                                    ttttAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTAt                                                          <  1:1792838/119‑1 (MQ=255)
                                                                                    ttttAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTAt                                                          >  2:1792838/1‑119 (MQ=255)
                                                                                                          gCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAAt                                                                   >  1:1826401/1‑88 (MQ=255)
                                                                                                          gCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAAt                                                                   <  2:1826401/88‑1 (MQ=255)
                                                                                                             acaaTCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTc                                                     <  2:1357384/99‑1 (MQ=255)
                                                                                                             acaaTCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTc                                                     >  1:1357384/1‑99 (MQ=255)
                                                                                                             acaaTCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGtt             <  2:1061813/139‑1 (MQ=255)
                                                                                                             acaaTCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGtt             >  2:695123/1‑139 (MQ=255)
                                                                                                               aaTCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTAt                                                          <  1:648372/92‑1 (MQ=255)
                                                                                                               aaTCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTAt                                                          >  2:648372/1‑92 (MQ=255)
                                                                                                               aaTCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGt                          <  2:1279138/124‑1 (MQ=255)
                                                                                                               aaTCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGt                          >  1:1279138/1‑124 (MQ=255)
                                                                                                                 tCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTcatcc                                                                                      <  1:49903/62‑1 (MQ=255)
                                                                                                                 tCAGGGACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTcatcc                                                                                      >  2:49903/1‑62 (MQ=255)
                                                                                                                    gggACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTc                                                     >  2:627036/1‑92 (MQ=255)
                                                                                                                    gggACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTc                                                     <  1:627036/92‑1 (MQ=255)
                                                                                                                    gggACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTAGCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCAtt      <  1:375655/139‑1 (MQ=255)
                                                                                                                     ggACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGAt                                                                                                      <  1:757826/42‑1 (MQ=255)
                                                                                                                     ggACAAAACAGATTATTGCATGACAAATTTCACTGTCGCGAt                                                                                                      >  2:757826/1‑42 (MQ=255)
                                                                                                                        cAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTaa                  >  1:186043/1‑123 (MQ=255)
                                                                                                                        cAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTaa                  <  2:186043/123‑1 (MQ=255)
                                                                                                                        cAAAACAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCAACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCATTCAGa  <  1:910561/139‑1 (MQ=255)
                                                                                                                         aaaaCAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAg                                                                              <  2:1393869/62‑1 (MQ=255)
                                                                                                                         aaaaCAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAg                                                                              >  1:1393869/1‑62 (MQ=255)
                                                                                                                         aaaaCAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTAt                                                          <  2:979562/82‑1 (MQ=255)
                                                                                                                         aaaaCAGATTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTAt                                                          >  1:979562/1‑82 (MQ=255)
                                                                                                                                 |                                                                                                                                 
TCTGTTGTTGTCTGTACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCACTGTCGCGATTTGCCCCACGTCATCCATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCATTCAGA  >  NC_000913/2644884‑2645142

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A