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 1,068,276 Δ1 bp intergenic (+22/+235) ymdF → / ← rutG KGG family protein/pyrimidine permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,068,2760G.100.0% 241.9 / NA 59intergenic (+22/+235)ymdF/rutGKGG family protein/pyrimidine permease
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (27/32);  total (27/32)

CAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCA  >  NC_000913/1068142‑1068410
                                                                                                                                      |                                                                                                                                      
cAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CAttt                                                                                                                                   <  1:613110/139‑1 (MQ=255)
                 cagcacggcGGGAGTAATTTCAAGAATGACCCGCAGCGCGAAACTTAAGCAGGTAAACAAGGTGGTAAGAGCAGGCACGGCAAAAGCGACAACGAACCGGTGTAATCAAGGACGAAT‑CATGGTTG‑CTGTAGCTCGTCaa                                                                                                                 <  1:528926/139‑1 (MQ=255)
                   gcacagcGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCaaaa                                                                                                               <  1:1646755/139‑1 (MQ=255)
                         cGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCt                                                                                                                       <  1:1366838/125‑1 (MQ=255)
                         cGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCt                                                                                                                       >  2:1366838/1‑125 (MQ=255)
                         cGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTc                                                                                                                   <  1:1291814/129‑1 (MQ=255)
                         cGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTc                                                                                                                   >  2:1291814/1‑129 (MQ=255)
                         cGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCAt                                                                                                         >  2:1648906/1‑139 (MQ=255)
                            gggTAATTTCAAGAATGACCCGCCGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAACGCCATCAc                                                                                                      >  2:528926/1‑139 (MQ=255)
                            gggTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAc                                                                                                      <  1:1648906/139‑1 (MQ=255)
                              gTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAccg                                                                                                    >  1:432856/1‑139 (MQ=255)
                                  tttCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCgg                                                                                                <  2:742569/139‑1 (MQ=255)
                                   ttCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTCG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGt                                                                                               <  2:197384/139‑1 (MQ=255)
                                         aaTGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  1:934061/139‑1 (MQ=255)
                                             aCCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGt                                                                                               >  1:500015/1‑129 (MQ=255)
                                             aCCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTAACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGt                                                                                               <  2:500015/129‑1 (MQ=255)
                                              cccGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  1:805818/134‑1 (MQ=255)
                                              cccGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  2:805818/1‑134 (MQ=255)
                                                  cAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGAt                                                                                >  2:336550/1‑139 (MQ=255)
                                                       cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACtga                                                                           >  2:1549181/1‑139 (MQ=255)
                                                       cgcATCTGAAGCAGGT‑AAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAcc                                                                                                     >  1:787394/1‑112 (MQ=255)
                                                       cgcATCTGAAGCAGGT‑AAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAcc                                                                                                     <  2:787394/112‑1 (MQ=255)
                                                               aaGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                                                   <  2:432856/139‑1 (MQ=255)
                                                                    ggTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  1:954659/1‑112 (MQ=255)
                                                                    ggTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:954659/112‑1 (MQ=255)
                                                                    ggTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAg                                                              <  1:336550/139‑1 (MQ=255)
                                                                    ggTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAg                                                              >  1:1769092/1‑139 (MQ=255)
                                                                      tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:1884096/110‑1 (MQ=255)
                                                                      tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  1:1884096/1‑110 (MQ=255)
                                                                         aaaaGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGc                                                         >  1:1227781/1‑139 (MQ=255)
                                                                                 gtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  1:1954198/139‑1 (MQ=255)
                                                                                      agCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg                                            <  2:975004/139‑1 (MQ=255)
                                                                                      agCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg                                            <  1:1549181/139‑1 (MQ=255)
                                                                                      agCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg                                            >  1:975004/1‑139 (MQ=255)
                                                                                        cAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 >  2:194888/1‑132 (MQ=255)
                                                                                        cAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  1:194888/132‑1 (MQ=255)
                                                                                                gCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 >  1:323342/1‑124 (MQ=255)
                                                                                                gCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  2:323342/124‑1 (MQ=255)
                                                                                                     aGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGcc                                                                                                           <  2:1789990/61‑1 (MQ=255)
                                                                                                     aGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGcc                                                                                                           >  1:1789990/1‑61 (MQ=255)
                                                                                                     aGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         >  2:1609790/1‑79 (MQ=255)
                                                                                                     aGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  1:1609790/79‑1 (MQ=255)
                                                                                                         aCAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCagaa                         <  2:1227781/139‑1 (MQ=255)
                                                                                                         aCAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCagaa                         <  1:1596167/139‑1 (MQ=255)
                                                                                                                accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAcc                                                                                                     <  1:1862917/55‑1 (MQ=255)
                                                                                                                accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAcc                                                                                                     >  2:1862917/2‑56 (MQ=255)
                                                                                                                    ggCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  2:1406635/104‑1 (MQ=255)
                                                                                                                    ggCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 >  1:1406635/1‑104 (MQ=255)
                                                                                                                        aaTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggt                                                                                       <  1:645999/62‑1 (MQ=255)
                                                                                                                        aaTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggt                                                                                       >  2:645999/1‑62 (MQ=255)
                                                                                                                        aaTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGCCAAAAAGCCATCACCGCCGGTTACCCGGTGGTGGATACTGATCACCAATGAAAGCTAGCCTGATGCGTGATGCTTAACAGGCCTACTAGAAGAtccgaatagatcg          >  1:1174954/1‑127 (MQ=255)
                                                                                                                         aTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCa                                                                                                          >  1:891611/1‑42 (MQ=255)
                                                                                                                         aTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCa                                                                                                          <  2:891611/42‑1 (MQ=255)
                                                                                                                             aTGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 >  1:796296/1‑95 (MQ=255)
                                                                                                                             aTGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  2:796296/95‑1 (MQ=255)
                                                                                                                              tGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 >  1:1674080/1‑94 (MQ=255)
                                                                                                                              tGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  2:1674080/94‑1 (MQ=255)
                                                                                                                              tGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTg    >  2:108434/1‑139 (MQ=255)
                                                                                                                                aCGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCa  <  2:1769092/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                      
CAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCA  >  NC_000913/1068142‑1068410

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