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
A5 F216 I0 R1 247 44.8 1629152 98.0% 1596568 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,880,851 T→A 14.3% intergenic (‑92/+35) leuE ← / ← dmlR leucine efflux protein/transcriptional activator of dmlA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,880,8510TA14.3% 94.5 / 9.3 35intergenic (‑92/+35)leuE/dmlRleucine efflux protein/transcriptional activator of dmlA
Reads supporting (aligned to +/- strand):  ref base T (14/16);  new base A (2/3);  total (16/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.27e-01

TGGCCCCAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGTCGCCAGCCTTGAAACATAAACGGCC  >  NC_000913/1880708‑1880997
                                                                                                                                               |                                                                                                                                                  
tGGCCCCAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAAc                                                                                                                                                >  4:239407/1‑148 (MQ=255)
   ccccAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTAAAACCTGa                                                                                                                                            <  2:255306/149‑1 (MQ=255)
    cccAACCAGATAGGTCCAGTAATTCAGAACCGCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGat                                                                                                                                           <  1:177088/149‑1 (MQ=255)
     ccAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTAAAACCTGat                                                                                                                                           <  3:192957/148‑1 (MQ=255)
          cAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAAc                                                                                                                                     <  2:109252/149‑1 (MQ=255)
                  tCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATTTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAAt                                                                                                                             >  2:135238/1‑149 (MQ=255)
                  tCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTAAAACCTGat                                                                                                                                           >  4:231298/1‑135 (MQ=255)
                  tCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTAAAACCTGat                                                                                                                                           <  3:231298/135‑1 (MQ=255)
                      gTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGa                                                                                                                          <  3:327477/148‑1 (MQ=255)
                       tAATTCAGAACCCCGTATTCAGAGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGACAATCAGGTTTTAACCTGATATCAACCCGATAATTGaa                                                                                                                         <  4:246057/148‑1 (MQ=255)
                         aTTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATc                                                                                                                       <  4:15621/148‑1 (MQ=255)
                         aTTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATc                                                                                                                       <  3:1358/148‑1 (MQ=255)
                                                     ttAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGt                                                                                                  >  1:238046/1‑141 (MQ=255)
                                                     ttAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGt                                                                                                  <  2:238046/141‑1 (MQ=255)
                                                     ttAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAAt                                                                                           >  3:297975/1‑148 (MQ=255)
                                                        aCCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCg                                                                                        <  4:81912/148‑1 (MQ=255)
                                                         ccTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCgg                                                                                       >  3:200924/1‑148 (MQ=255)
                                                         ccTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCgg                                                                                       >  4:206143/1‑148 (MQ=255)
                                                           tctTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAAtt                                                                                                                            >  1:288879/1‑109 (MQ=255)
                                                           tctTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCAATAAtt                                                                                                                            <  2:288879/109‑1 (MQ=255)
                                                              ttAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGt                                                                                  >  4:56337/1‑148 (MQ=255)
                                                              ttAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTg                                                                                 >  2:203173/1‑149 (MQ=255)
                                                                 aTTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCt                                                                               >  4:136013/1‑148 (MQ=255)
                                                                       tttCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCaa                                                                         >  3:134135/1‑148 (MQ=255)
                                                                            aTCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATAc                                                                    <  4:200924/148‑1 (MQ=255)
                                                                             tCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACt                                                                   <  3:56337/148‑1 (MQ=255)
                                                                             tCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTg                                                                  >  1:77008/1‑149 (MQ=255)
                                                                              cATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTg                                                                  <  4:7401/148‑1 (MQ=255)
                                                                                         aaaGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTc                                                      <  2:77008/149‑1 (MQ=255)
                                                                                          aaGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTc                                                      <  3:136013/148‑1 (MQ=255)
                                                                                           aGGTGAATATGCTAACCAATCTGTAGAGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCt                                                     <  4:297975/148‑1 (MQ=255)
                                                                                                                   aGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACg                            >  1:46589/1‑149 (MQ=255)
                                                                                                                                     ataTCAGGTTAAAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGTCGCCAGCCTTGAAACAt          >  2:344365/3‑149 (MQ=255)
                                                                                                                                      aaTCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGTCGCCAGCCTTGAAACATa         <  2:196826/149‑1 (MQ=255)
                                                                                                                                          aGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGTCGCCAGCCTTGAAACATAAACg     >  2:17457/1‑149 (MQ=255)
                                                                                                                                              tttAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGTCGCCAGCCTTGAAACATAAACGGcc  >  3:376104/1‑148 (MQ=255)
                                                                                                                                               |                                                                                                                                                  
TGGCCCCAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGTCGCCAGCCTTGAAACATAAACGGCC  >  NC_000913/1880708‑1880997

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A