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
A8 F1 I1 R1 771 44.8 2153074 94.1% 2026042 109.1

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.94.3% 131.3 / 2.1 35intergenic (+235/‑131)fadL/yfdFlong‑chain fatty acid outer membrane transporter/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base . (13/20);  total (14/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.07e-01

CAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAAT  >  NC_000913/2462746‑2462990
                                                                                                                                       |                                                                                                             
cAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccc                                                                                                            <  1:701874/139‑1 (MQ=255)
       ccTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccccctgg                                                                                                     <  2:417797/139‑4 (MQ=255)
                   ttGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCt                                                                                        >  2:563379/1‑139 (MQ=255)
                      cccTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCAt                                                                                     <  2:605055/139‑1 (MQ=255)
                            cAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGGTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                               <  2:1014948/139‑1 (MQ=255)
                                tCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAAt                                                                           >  1:241371/1‑139 (MQ=255)
                                 cAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAAtt                                                                          >  2:312504/1‑139 (MQ=255)
                                    tAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccccctgg                                                                                                     <  1:29352/110‑4 (MQ=255)
                                    tAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccccctgg                                                                                                     >  2:29352/1‑107 (MQ=255)
                                    tAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccc                                                                                                          >  2:965758/1‑105 (MQ=255)
                                    tAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccc                                                                                                          <  1:965758/105‑1 (MQ=255)
                                       gCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCGGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                    <  2:552585/139‑1 (MQ=255)
                                       gCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAAGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCGAGGAAACT‑CACCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                    <  2:661398/139‑1 (MQ=255)
                                            aTCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATAGT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                               >  1:526817/1‑139 (MQ=255)
                                            aTCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                               <  2:241371/139‑1 (MQ=255)
                                                acaGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCC‑‑GGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCtaaa                                                          >  1:250296/1‑139 (MQ=255)
                                                       aaCCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATg                                                    >  2:836658/1‑139 (MQ=255)
                                                       aaCCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGCCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccccc                                                                                                        >  1:56532/1‑88 (MQ=255)
                                                       aaCCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGCCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccccc                                                                                                        <  2:56532/88‑1 (MQ=255)
                                                              aGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATAGT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGttt                                             <  2:526817/139‑1 (MQ=255)
                                                              aGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                    >  1:180540/1‑116 (MQ=255)
                                                              aGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                    <  2:180540/116‑1 (MQ=255)
                                                                   aaGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                        <  1:563379/139‑1 (MQ=255)
                                                                          atTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                        <  2:855601/132‑1 (MQ=255)
                                                                          atTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                        >  1:855601/1‑132 (MQ=255)
                                                                          atTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTa                                 <  1:746271/139‑1 (MQ=255)
                                                                                aGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccc                                                                                                          <  1:60896/61‑1 (MQ=255)
                                                                                aGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccc                                                                                                          >  2:60896/1‑61 (MQ=255)
                                                                                aGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAg                                     <  2:298593/129‑1 (MQ=255)
                                                                                aGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAg                                     >  1:298593/1‑129 (MQ=255)
                                                                                 ggCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAtt                          <  2:338675/139‑1 (MQ=255)
                                                                                 ggCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAtt                          <  1:312504/139‑1 (MQ=255)
                                                                                    gTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTgcg                                                                                          >  1:530885/1‑72 (MQ=255)
                                                                                    gTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTgcg                                                                                          <  2:530885/72‑1 (MQ=255)
                                                                                    gTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAgg                       <  2:164879/139‑1 (MQ=255)
                                                                                      tCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                               <  2:543531/81‑1 (MQ=255)
                                                                                      tCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                               >  1:543531/1‑81 (MQ=255)
                                                                                               ccTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATAtt            <  1:836658/139‑1 (MQ=255)
                                                                                                       aaGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCC‑‑GGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACaaa   <  2:250296/139‑1 (MQ=255)
                                                                                                       aaGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACaa    <  1:361686/139‑1 (MQ=255)
                                                                                                         gagTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGTTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaat  >  2:807209/1‑139 (MQ=255)
                                                                                                              tACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                        >  1:950671/1‑96 (MQ=255)
                                                                                                              tACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                        <  2:950671/96‑1 (MQ=255)
                                                                                                                                  aTACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                               <  2:564790/37‑1 (MQ=255)
                                                                                                                                  aTACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                               >  1:564790/1‑37 (MQ=255)
                                                                                                                                       |                                                                                                             
CAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAAT  >  NC_000913/2462746‑2462990

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A