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
A4 F1 I2 R1 67 32.5 1435938 95.9% 1377064 112.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,406,097 (T)5→6 coding (545/939 nt) lrhA ← transcriptional repressor of flagellar, motility and chemotaxis genes

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,406,0921.T78.4% 141.3 / 33.5 51coding (550/939 nt)lrhAtranscriptional repressor of flagellar, motility and chemotaxis genes
Reads supporting (aligned to +/- strand):  ref base . (5/6);  new base T (22/18);  total (27/24)
Fisher's exact test for biased strand distribution p-value = 7.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01

CCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCATA  >  NC_000913/2405960‑2406225
                                                                                                                                     |                                                                                                                                     
ccGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTAATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGCGGGATCGGCTCGCC‑ttttt                                                                                                                                  <  1:6426/138‑1 (MQ=255)
ccGCACGAACGCCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTAATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑ttttt                                                                                                                                  >  2:6426/1‑138 (MQ=255)
   cACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑ttttttgca                                                                                                                              >  1:339027/1‑135 (MQ=255)
   cACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGACCGGCTCGCC‑ttttttgca                                                                                                                              <  2:397061/139‑5 (MQ=255)
     cGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAat                                                                                                                             <  1:572442/139‑1 (MQ=255)
               gAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCg                                                                                                                   <  2:339027/139‑1 (MQ=255)
                   cGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTgcg                                                                                                              <  1:643612/139‑1 (MQ=255)
                    gTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTgcg                                                                                                              <  1:652041/139‑1 (MQ=255)
                               aTAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAgtg                                                                                                   <  2:564150/139‑1 (MQ=255)
                                       gTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATACGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGa                                                                                          >  2:237381/1‑139 (MQ=255)
                                                           ttattaAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAgtg                                                                                                   >  1:314949/1‑111 (MQ=255)
                                                           ttattaAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAgtg                                                                                                   <  2:314949/111‑1 (MQ=255)
                                                               taAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATACGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTaaa                                                                  <  1:237381/139‑1 (MQ=255)
                                                                      cGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGa                                                            <  2:381662/139‑1 (MQ=255)
                                                                        ccAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAg                                                          >  1:157091/1‑139 (MQ=255)
                                                                        ccAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAg                                                          >  2:530004/1‑139 (MQ=255)
                                                                         cAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAgg                                                         <  2:157091/139‑1 (MQ=255)
                                                                                 tatCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATggg                                                 >  1:381165/1‑139 (MQ=255)
                                                                                        aaaCGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTAc                                          >  1:241628/1‑139 (MQ=255)
                                                                                             ggCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTg                                                                                                                <  1:79546/64‑1 (MQ=255)
                                                                                             ggCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTg                                                                                                                >  2:79546/1‑64 (MQ=255)
                                                                                              gCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCaa                                    >  2:457475/1‑139 (MQ=255)
                                                                                              gCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCaa                                    >  1:570219/1‑139 (MQ=255)
                                                                                                      catcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGtt                                            >  2:243825/1‑123 (MQ=255)
                                                                                                      catcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGtt                                            <  1:243825/123‑1 (MQ=255)
                                                                                                       atcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTgcg                                                                                                              >  2:410163/1‑56 (MQ=255)
                                                                                                       atcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTgcg                                                                                                              <  1:410163/56‑1 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAg                                                                                         <  1:271437/76‑1 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAg                                                                                         >  2:271437/1‑76 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTc                                                                             <  1:238010/88‑1 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTc                                                                             >  2:238010/1‑88 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTcc                          >  1:682444/1‑139 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGtt                                                                              >  1:65729/1‑86 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGtt                                                                              <  2:65729/86‑1 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACg                                                                >  1:363538/1‑100 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACg                                                                <  2:363538/100‑1 (MQ=255)
                                                                                                        tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCt                         >  1:581487/1‑139 (MQ=255)
                                                                                                            gCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATc                                      <  2:569756/123‑1 (MQ=255)
                                                                                                            gCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATc                                      >  1:569756/1‑123 (MQ=255)
                                                                                                             cAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGATGATGGGTGGTTACCATCAAATCCAGTTCCTGGGa                     >  1:458451/1‑139 (MQ=255)
                                                                                                              aaTACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGAt                    <  1:530004/139‑1 (MQ=255)
                                                                                                               aTACAAGAGGGATCGGCGCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGAAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTc                  <  2:404813/139‑1 (MQ=255)
                                                                                                                tACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCa                               <  2:574230/126‑1 (MQ=255)
                                                                                                                tACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCa                               >  1:574230/1‑126 (MQ=255)
                                                                                                                tACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTc                  >  2:336023/1‑139 (MQ=255)
                                                                                                                      agGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCAt            <  2:241628/139‑1 (MQ=255)
                                                                                                                          aTCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCt        >  2:564547/1‑139 (MQ=255)
                                                                                                                          aTCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCt        >  2:626488/1‑139 (MQ=255)
                                                                                                                          aTCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCt        >  2:182098/1‑139 (MQ=255)
                                                                                                                          aTCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTg       >  2:434170/1‑139 (MQ=255)
                                                                                                                          aTCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTg       <  1:434170/139‑1 (MQ=255)
                                                                                                                             ggCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGcc     >  1:190309/1‑139 (MQ=255)
                                                                                                                               cTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCat   >  1:419952/1‑139 (MQ=255)
                                                                                                                                tCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCata  <  2:419952/139‑1 (MQ=255)
                                                                                                                                tCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCata  <  1:332414/139‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                     
CCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCATA  >  NC_000913/2405960‑2406225

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