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
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,462,889 (C)9→8 intergenic (+243/‑123) fadL → / → yfdF long‑chain fatty acid outer membrane transporter/uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,462,8810C.100.0% 196.6 / NA 48intergenic (+235/‑131)fadL/yfdFlong‑chain fatty acid outer membrane transporter/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (21/27);  total (21/27)

TGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCAT  >  NC_000913/2462744‑2463013
                                                                                                                                          |                                                                                                                                    
tGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTCCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcc                                                                                                                                     >  2:896637/1‑139 (MQ=255)
  cAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccc                                                                                                                                   <  1:849208/139‑1 (MQ=255)
    aaCAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccc                                                                                                                                 <  1:499325/139‑1 (MQ=255)
     aCAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTccccccc                                                                                                                                >  2:942737/1‑139 (MQ=255)
      cAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTccccccc                                                                                                                                <  2:1374892/139‑1 (MQ=255)
       aGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccc                                                                                                                                 >  1:1193281/1‑136 (MQ=255)
       aGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccc                                                                                                                                 <  2:1193281/136‑1 (MQ=255)
                 cAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTCCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATtgtg                                                                                                                   <  1:896637/139‑1 (MQ=255)
                   gCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTgcg                                                                                                                 >  2:1174233/1‑139 (MQ=255)
                   gCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTgcg                                                                                                                 <  1:942737/139‑1 (MQ=255)
                   gCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTgcg                                                                                                                 <  1:1600656/139‑1 (MQ=255)
                       gCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATtgtg                                                                                                                   >  1:366226/1‑133 (MQ=255)
                       gCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATtgtg                                                                                                                   <  2:366226/133‑1 (MQ=255)
                       gCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCa                                                                                                             >  2:265402/1‑139 (MQ=255)
                         ccTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATa                                                                                                           <  1:715127/139‑1 (MQ=255)
                              cAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                                                      <  2:1418720/139‑1 (MQ=255)
                                     aTAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATa                                                                                                           >  1:100586/1‑127 (MQ=255)
                                     aTAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATa                                                                                                           <  2:100586/127‑1 (MQ=255)
                                         gCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                           <  2:634380/139‑1 (MQ=255)
                                         gCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                           <  1:1412878/139‑1 (MQ=255)
                                            gTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAgg                                                                                        <  2:934157/139‑1 (MQ=255)
                                                    aGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                      >  1:257253/1‑133 (MQ=255)
                                                    aGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                      <  2:257253/133‑1 (MQ=255)
                                                       cAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCtaaataaa                                                                             >  1:8751/1‑139 (MQ=255)
                                                       accttcagAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCtaaataaa                                                                             >  1:466918/8‑139 (MQ=255)
                                                          aCCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                           >  1:196099/1‑122 (MQ=255)
                                                          aCCTGAAGGGAAAGGCATA‑ATTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                           <  2:196099/122‑1 (MQ=255)
                                                           ccTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACt                                                                                                       >  1:186696/1‑109 (MQ=255)
                                                           ccTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACt                                                                                                       <  2:186696/109‑1 (MQ=255)
                                                           ccTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAg                                                                         <  1:1174233/139‑1 (MQ=255)
                                                                           ta‑tTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAgg                                                                                        >  1:93020/1‑108 (MQ=255)
                                                                           ta‑tTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAgg                                                                                        <  2:93020/108‑1 (MQ=255)
                                                                                  cAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCa                                                   <  2:8751/139‑1 (MQ=255)
                                                                                  cAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCa                                                   <  2:466918/139‑1 (MQ=255)
                                                                                    ggCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAtt                                                 <  2:217108/139‑1 (MQ=255)
                                                                                       gTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGa                                                                                            >  1:394626/1‑93 (MQ=255)
                                                                                       gTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGa                                                                                            <  2:394626/93‑1 (MQ=255)
                                                                                       gTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAgg                                              <  1:1287649/139‑1 (MQ=255)
                                                                                         tCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTa                                            <  2:572493/139‑1 (MQ=255)
                                                                                                  ccTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACt                                                                                                       <  2:1344856/71‑1 (MQ=255)
                                                                                                  ccTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACt                                                                                                       >  1:1344856/1‑71 (MQ=255)
                                                                                                     tctcAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTa                               >  1:1179410/1‑139 (MQ=255)
                                                                                                         aaaGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACaa                           <  2:1179410/139‑1 (MQ=255)
                                                                                                           agagTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACaaa                          >  1:587862/1‑139 (MQ=255)
                                                                                                                ttACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaatcaat                     >  1:136570/1‑139 (MQ=255)
                                                                                                                       tCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATg              >  1:28518/1‑139 (MQ=255)
                                                                                                                       tCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCGCATACACTCAAATTAAAGATAGGTTCTAAATGAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATg              >  2:989795/1‑139 (MQ=255)
                                                                                                                         tGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGt                                                           <  1:1517017/92‑1 (MQ=255)
                                                                                                                         tGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGt                                                           >  2:1517017/1‑92 (MQ=255)
                                                                                                                         tGCATTTCCAGGATACT‑CCCCCCCCTGGCCATTGTGCCCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGGGTTTTTTGATAGTCTATTTCATTAGGTAATTTATATTTTTAAAAAATCAATCAAAATGGa            >  1:856692/1‑139 (MQ=255)
                                                                                                                         tGCATTTCCAGGATACT‑‑CCCCCCCTGGCTATTGTgcg                                                                                                                 <  2:871853/37‑1 (MQ=255)
                                                                                                                         tGCATTTCCAGGATACT‑‑CCCCCCCTGGCTATTGTgcg                                                                                                                 >  1:871853/1‑37 (MQ=255)
                                                                                                                              ttCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGtt                                                                     <  1:20020/77‑1 (MQ=255)
                                                                                                                              ttCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGtt                                                                     >  2:20020/1‑77 (MQ=255)
                                                                                                                                   ggATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCAt  <  2:587862/139‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                    
TGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATA‑TTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCAT  >  NC_000913/2462744‑2463013

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