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
A1 F1 I1 R1 773 79.9 4112934 92.2% 3792125 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,792,267 C→T *155* (TAG→TAA)  nlpC ← putative C40 clan peptidase lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,792,2670CT100.0% 148.9 / NA 47*155* (TAG→TAA) nlpCputative C40 clan peptidase lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/25);  total (22/25)

GTCCTTTTTTTAGATTATCCTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATACTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGTATCGTAAATACCTACAT  >  NC_000913/1792141‑1792388
                                                                                                                              |                                                                                                                         
gTCCTTTTTTTAGATTATCCTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGtctc                                                                                                               >  1:882663/1‑139 (MQ=255)
gTCCTTTTTTTAGATTATCCTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGtctc                                                                                                               >  1:620064/1‑139 (MQ=255)
                  ccTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTc                                                                                             <  2:907644/139‑1 (MQ=255)
                   cTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCt                                                                                            <  2:882663/139‑1 (MQ=255)
                       ttATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCa                                                                                        <  2:620064/139‑1 (MQ=255)
                           aaaCGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAg                                                                                    >  1:70038/1‑139 (MQ=255)
                           aaaCGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAg                                                                                    >  1:599768/1‑139 (MQ=255)
                                aataatCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGGTTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACAtt                                                                               >  2:1811300/1‑139 (MQ=255)
                                aataatCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAACTTTTTCTGCCAATAGACAtt                                                                               >  2:730361/1‑139 (MQ=255)
                                aataatCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACAtt                                                                               >  2:474774/1‑139 (MQ=255)
                                  taatCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTAt                                                                             <  2:599768/139‑1 (MQ=255)
                                   aatCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATc                                                                            <  1:552259/139‑1 (MQ=255)
                                               gAACTTTTTTCTGCAAATTGCTTCTGTATTCAGGATTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGAAATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGACAATAGACATTATCAAGTGAGGAACg                                                                <  2:218459/139‑1 (MQ=255)
                                                      tGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACt                                                         <  1:1027766/139‑1 (MQ=255)
                                                            cAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGcc                                                                                                        <  2:676080/86‑1 (MQ=255)
                                                            cAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGcc                                                                                                        >  1:676080/1‑86 (MQ=255)
                                                                         tATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGa                                                                                                                       <  2:91684/58‑1 (MQ=255)
                                                                         tATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGa                                                                                                                       >  1:91684/1‑58 (MQ=255)
                                                                         tATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGt                                      >  2:611596/1‑139 (MQ=255)
                                                                           ttCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAg                                                                                    <  1:1090085/91‑1 (MQ=255)
                                                                           ttCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAg                                                                                    >  2:1090085/1‑91 (MQ=255)
                                                                                 aGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCg                                       <  1:33627/130‑1 (MQ=255)
                                                                                 aGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCg                                       >  2:33627/1‑130 (MQ=255)
                                                                                          aCGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAAtttt                                                                                               <  2:1561129/65‑1 (MQ=255)
                                                                                          aCGGCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAAtttt                                                                                               >  1:1561129/1‑65 (MQ=255)
                                                                                            ggCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTccc                                                      <  1:665730/104‑1 (MQ=255)
                                                                                            ggCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTccc                                                      >  2:665730/1‑104 (MQ=255)
                                                                                            ggCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGt                   <  2:1481743/139‑1 (MQ=255)
                                                                                             gCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCtt                                                    <  2:1714170/105‑1 (MQ=255)
                                                                                             gCGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCtt                                                    >  1:1714170/1‑105 (MQ=255)
                                                                                              cGATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGAT‑AATTGGTTGTTGGTATc                <  1:730361/139‑1 (MQ=255)
                                                                                               gATGTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGTATc                <  1:1251839/139‑1 (MQ=255)
                                                                                                 tGTATCATCGCCGTCCATTTTTCTACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCt                                                                                            <  2:1332551/61‑1 (MQ=255)
                                                                                                 tGTATCATCGCCGTCCATTTTTCTACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCt                                                                                            >  1:1332551/1‑61 (MQ=255)
                                                                                                  gTATCATCGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGTATCGTa             <  2:70038/139‑1 (MQ=255)
                                                                                                        tcGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTc                                                                                             <  2:1819787/53‑1 (MQ=255)
                                                                                                        tcGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTc                                                                                             >  1:1819787/1‑53 (MQ=255)
                                                                                                        tcGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCAt                                                             >  2:530242/1‑85 (MQ=255)
                                                                                                        tcGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCAt                                                             <  1:530242/85‑1 (MQ=255)
                                                                                                        tcGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGa                                   >  1:1335874/1‑111 (MQ=255)
                                                                                                        tcGCCGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGa                                   <  2:1335874/111‑1 (MQ=255)
                                                                                                           ccGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGgt                          <  1:1425267/117‑1 (MQ=255)
                                                                                                           ccGTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGgt                          >  2:1425267/1‑117 (MQ=255)
                                                                                                             ggccATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTAt                                                                             <  1:1068472/62‑1 (MQ=255)
                                                                                                             gTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATATACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGTATCGTAAATACCTACAt  >  1:261785/1‑139 (MQ=255)
                                                                                                             gTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTAt                                                                             >  2:1068472/1‑64 (MQ=255)
                                                                                                             gTCCATTTTTCGACATATTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGTATCGTAAATACCTACAt  <  1:474774/139‑1 (MQ=255)
                                                                                                                              |                                                                                                                         
GTCCTTTTTTTAGATTATCCTGATTATAAACGAATAATCCATTTACGGAATTTTTGTCTGCAAAATACTACTGTATTCAGGAGTAAATGGACGGCGATGTATCATCGCCGTCCATTTTTCGACATACTAGATTCGTCTCGCCTGCCAGAAATTTTTCTGCCAATAGACATTATCAAGTGAGGAACGCATCACTCCCTTGCTGGTAGAGGCGTGGATAAATTGGTTGTTGGTATCGTAAATACCTACAT  >  NC_000913/1792141‑1792388

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