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
A22 F68 I1 R1 31 72.2 3191514 95.4% 3044704 126.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA BS168_reference_genome 1,317,158 (T)5→6 coding (257/258 nt) yjpA ← putative enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*BS168_reference_genome1,317,1531.T96.0% 165.2 / 0.1 50intergenic (+24/+4)phrA/yjpAsecreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme
Reads supporting (aligned to +/- strand):  ref base . (2/0);  new base T (21/27);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 2.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

GTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑C‑T‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTC  >  BS168_reference_genome/1317021‑1317275
                                                                                                                                       |                                                                                                                           
gttgCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑G‑t‑ctttt                                                                                                                      >  5:136691/1‑138 (MQ=255)
     tCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAAAAGCAAAAACAGAACGGAAAACATTTCATATTTCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑G‑T‑Cttttttatt                                                                                                                 >  7:109408/1‑136 (MQ=255)
          gCGGTCGGGGTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATttctt                                                                                                                <  1:228686/138‑1 (MQ=255)
                           tACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCtttt                                                                                                <  4:182649/137‑1 (MQ=255)
                            aCTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCa                                                                                                       <  8:73737/129‑1 (MQ=255)
                            aCTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCa                                                                                                       >  7:73737/1‑129 (MQ=255)
                             cgcAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTATTCAGCTTCCATTCTTTTATc                                                                                             >  2:361441/3‑138 (MQ=255)
                                aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGt                                                                                           <  7:114082/137‑1 (MQ=255)
                                  gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAATGGAAAACATTTCATATTGCGGCACGCAATCAATCATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTAATCGTCAGc                                                                                       >  5:160659/1‑139 (MQ=255)
                                  gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCAAATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGc                                                                                       >  4:109154/1‑139 (MQ=255)
                                     aTGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCATCTTCCAATCTTTTATAGTAAGCTc                                                                                     >  2:201770/1‑138 (MQ=255)
                                     aTGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCa                                                                                    <  1:201770/139‑1 (MQ=255)
                                     aTGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCa                                                                                    <  4:47686/139‑1 (MQ=255)
                                       ggTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCag                                                                                   >  8:72253/1‑138 (MQ=255)
                                        gTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCag                                                                                   >  4:226223/1‑137 (MQ=255)
                                            aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCTTCAGCTCAGAAGATc                                                                             >  5:289893/1‑139 (MQ=255)
                                            aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc                                                                             >  6:338441/1‑139 (MQ=255)
                                            aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc                                                                             >  6:332782/1‑139 (MQ=255)
                                                  gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGGACGCAATCAATCATGATGCATAAAAAAAGACCCTTAGGGGTC‑TGTTTTATGGCTTCAGCTTCCAGTCTTTTATCGTCAGCTCAGAAGATCCACTTg                                                                       >  3:354129/1‑139 (MQ=255)
                                                     aaaCAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGcc                                                                     <  5:262916/138‑1 (MQ=255)
                                                       aCAGCAAACACAGAAGTGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGccacc                                                                  <  5:370283/139‑1 (MQ=255)
                                                       aCAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCATCTCAGAAGATCCACTTGccacc                                                                  <  1:301606/139‑1 (MQ=255)
                                                            aaaCACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCg                                                              >  7:146740/1‑138 (MQ=255)
                                                                 caGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCg                                                        <  7:318026/139‑1 (MQ=255)
                                                                  aGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAg                                                                >  6:126790/1‑130 (MQ=255)
                                                                  aGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAg                                                                <  5:126790/130‑1 (MQ=255)
                                                                   gAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCa                                                      <  3:226223/139‑1 (MQ=255)
                                                                                ttCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTAAGAAGATCCCCATGACACCCGCTGATACGCAATGCCGCTATCCg                                         >  2:152306/1‑139 (MQ=255)
                                                                                  cATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCGCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCt                                       <  1:152306/139‑1 (MQ=255)
                                                                                   atatTGCCGCACGCAATCTAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCt                                       <  1:270087/138‑1 (MQ=255)
                                                                                    tatTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGc                                     <  5:12476/139‑1 (MQ=255)
                                                                                        gCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCt                                       <  2:219851/133‑1 (MQ=255)
                                                                                        gCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCt                                       >  1:219851/1‑133 (MQ=255)
                                                                                        gCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCctct                                 >  3:83527/1‑139 (MQ=255)
                                                                                         cGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCctct                                 <  5:332782/138‑1 (MQ=255)
                                                                                         cGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCctct                                 <  5:338441/138‑1 (MQ=255)
                                                                                                 aaTCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGt                                                                                           <  5:272257/72‑1 (MQ=255)
                                                                                                 aaTCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGt                                                                                           >  6:272257/1‑72 (MQ=255)
                                                                                                  aTCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAAt                       <  7:55287/139‑1 (MQ=255)
                                                                                                           gatgCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg               <  8:146740/138‑1 (MQ=255)
                                                                                                            atgCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt             <  8:109408/139‑1 (MQ=255)
                                                                                                            atgCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt             <  4:384236/139‑1 (MQ=255)
                                                                                                             tgCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGc                                     <  3:103805/114‑1 (MQ=255)
                                                                                                             tgCATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGc                                     >  4:103805/1‑114 (MQ=255)
                                                                                                               cATAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGa           >  5:133739/1‑138 (MQ=255)
                                                                                                                 tAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa         >  1:20989/1‑138 (MQ=255)
                                                                                                                 tAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa         >  6:231204/1‑138 (MQ=255)
                                                                                                                 tAAAAAAAGACCCTTAGGGGTCTT‑TTTTATTTATTCAGCTTCCATTGTTTTATCGTCAGCTCAGAAGATCCCCTTGCCCCCCGCGGCTCCCCCTGGCCGAGTTCCGCGGCCGCGTGCAGGTAATCAGCTTGGATGGCa         >  2:191664/1‑138 (MQ=255)
                                                                                                                     aaaaGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGCTCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGc    <  6:113479/139‑1 (MQ=255)
                                                                                                                     aaaaGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGc    <  8:35165/139‑1 (MQ=255)
                                                                                                                       aaGACCCTTAGGGGTCTT‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTc  <  2:285185/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                           
GTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑C‑T‑TTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTC  >  BS168_reference_genome/1317021‑1317275

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A