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
A29 F119 I0 R1 76 56.4 2152892 90.0% 1937602 142.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase subunit beta

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,184,5430CA98.4% 121.6 / ‑6.0 48P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (0/1);  major base A (18/27);  minor base G (0/1);  total (18/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATC  >  NC_000913/4184407‑4184679
                                                                                                                                        |                                                                                                                                        
gCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTggg                                                                                                                                    <  1:263838/143‑1 (MQ=255)
ccGGTTAAACGGCATATCCAACCTGGTGACTAGATGGCAGGACGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGCTATGCCTCACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTggg                                                                                                                                    <  2:310919/142‑1 (MQ=255)
 agtcaaaaCGCCGGATCCAGCCCGGTGACAAGACGGGAGGTCGTCACGGTAACAAGGGTGTAAGTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGc                                                                                                                                   <  1:28956/138‑1 (MQ=255)
           ccGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGGTAGGCCTTACGATGAAAAGGGTACTCCTGCAGACATCGTACAGGACCAACGGGGCGGACCggcgc                                                                                                                         >  1:776159/1‑139 (MQ=255)
                  cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                  >  2:581359/1‑143 (MQ=255)
                  cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAAAGGGACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                  >  2:927527/1‑143 (MQ=255)
                   aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTACGTTCTAAGATCAACCCGATCGAAGACAGGCCTAACGATGAAAACGGTCCGCGGATAGACAACGAAATGAACCAGACGGGCGTGCCGACACGTATGAAc                                                                                                                 >  2:954123/1‑143 (MQ=255)
                   aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGCTCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGACTCGTATGAAc                                                                                                                 >  2:827897/1‑143 (MQ=255)
                   aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAGGAAc                                                                                                                 >  1:772288/1‑143 (MQ=255)
                       tGGTGACAAGATGGCAGGGCGTCACGGTCACAAGGGTGTAATTGCTAACATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                             <  1:380651/143‑1 (MQ=255)
                       cggTGACAACATGGCAGGTCGCCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGACAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                             <  1:151144/142‑1 (MQ=255)
                                 aTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCt                                                                                                   >  1:529854/1‑143 (MQ=255)
                                     cAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaa                                                                                               <  1:509279/143‑1 (MQ=255)
                                      aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                              <  1:91782/143‑1 (MQ=255)
                                        gcggtcACGGTAGCAAGGGTGGAATTTCTAAGATCGACGCGATCGAAGATAGGCCTTACGATGAAAGCGGTACGCCGGTAGACATCGTACTGGACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAcc                                                                                            <  2:983444/140‑1 (MQ=255)
                                              aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCATTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCACGTATGAACATCGGTCAGAAGCTCGAAACCCAccgg                                                                                      >  2:133438/1‑141 (MQ=255)
                                                ggTAACAAGGGTGTAAATTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTggg                                                                                    <  1:152650/143‑1 (MQ=255)
                                                  tAACAAGGGTGTAATTTCCACGACCAACCCGATCGAACATATACCGTAGGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTa                                                                                  <  1:88834/143‑1 (MQ=255)
                                                     cAAGGGTGGCATTTCTGAGATCGGCCCTATCGATGATATGTCTTANGATGAAAGCGGTACGCCGGTAGACATCGTNCTGAACCAGCTGGGGGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATgg                                                                               <  2:724744/143‑1 (MQ=255)
                                                           tgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGGGa                                                                         >  1:717915/1‑143 (MQ=255)
                                                           tgcaaTTTCGAAGATCACCCCGATCGAAGATATGCCTCACGATGGACACGGTAGGCCTGTAGACATCGTACTGCACCAGCTGGGCGTACCGTCTCGTAAGAACATCGGTCACGGCCTCGAAACCCACCTGGGGATGGCTGCGa                                                                         <  1:250801/140‑1 (MQ=255)
                                                             tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGCACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCGTCGAAACCGCCCTGGGTATAGATGCGaaa                                                                       >  2:48309/1‑143 (MQ=255)
                                                              aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACGAGCTGGGCGTACAGTCCCGTATGAACATCGGTCAGATCCTCGAAACACACATGGGTATGGCTGCGAAAg                                                                      >  1:290455/1‑143 (MQ=255)
                                                              aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                      <  1:1046209/143‑1 (MQ=255)
                                                                     aaGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCgg                                                               >  2:65524/1‑143 (MQ=255)
                                                                        aTCAACCTGATTGAAGATATGTCTTACGATGAAAACGGTACGCCGGTAGACAGCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                            <  1:331766/143‑1 (MQ=255)
                                                                           aaCTCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGTTCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                         <  2:577990/143‑1 (MQ=255)
                                                                           aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                         <  2:1006155/143‑1 (MQ=255)
                                                                             accGATCAAAGATAGGCCTTACGAGGAAGACGGTACGCCGGTAGACATCGTACTGCAGCGGCTGGGCGTACCGTCTCGTATGAACAGCGGTCAGGTCCTCGAAACCCACCTGCGTATGGCTGCGAAGGGTATCGGCGACAAGa                                                       <  2:524013/142‑1 (MQ=255)
                                                                                  tCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                                  <  1:123828/143‑1 (MQ=255)
                                                                                  tCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACAGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                                  <  1:649680/143‑1 (MQ=255)
                                                                                       gagacgCCTTACGAGGAAAACGGGACGCCGGTAGACGTCGTACTGAACCAGCTGAGCGTACCGTCTCGTATGAACATCGGTCAGAGCCTCGAAACCCTCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCAt                                             <  1:58069/138‑1 (MQ=255)
                                                                                       gATATGCCTTAAGATGAGAACGGTACGCCGGTAGACATAGGACGGAGGCAGGCGGGCGTACCGTCGCGTATGAACATCGGTCAGAGCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCAt                                             <  1:129276/143‑1 (MQ=255)
                                                                                            gCCTTACGATGAAAACGGTACGCCGGTAGACCTCGTACTGACCCAGCTGGACGTACCGTCTCGTATGAAAATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGa                                        >  1:179736/1‑143 (MQ=255)
                                                                                              cTTACGATGAAAACGGTACGCCAGTAGACATCGTACTGAGCCAGCTGGGCGTTCCGACCCACATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                      <  1:491831/143‑1 (MQ=255)
                                                                                                   gATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCAAAAAGAACAACGGCATGCTGAAAcagca                                 >  2:941517/1‑143 (MQ=255)
                                                                                                    aTGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTGTGGCTGCGAGAGGTATCGGCGACAAGAGCAACGCCATGCTGAAGccgcag                                >  2:969915/1‑143 (MQ=255)
                                                                                                     tGAAAACGGCACGCCCGTAGACATCGTACTTAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGACCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACagcagc                               <  1:318705/143‑1 (MQ=255)
                                                                                                      gAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCCTGCTGAAACAgcagca                              >  2:898577/1‑143 (MQ=255)
                                                                                                      gAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGTATGGCGGCGAAAGGTATCGGCGACAAGATCCACGCCATGCTGAAAAAgcagca                              >  2:270968/1‑143 (MQ=255)
                                                                                                              tatgcgggTAGACAGCGTACTGGGCGAGCTGGGCGTACCGTCTGGTATGAACATCGGTCAGATCCGCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                      <  2:768082/137‑1 (MQ=255)
                                                                                                               aCGTCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCGCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcgc                     <  2:783888/143‑1 (MQ=255)
                                                                                                                   cGGTCGACATCGTACTGAACCCGCTGCGCGTACCGTCTCGCATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGaaa                 <  1:207180/143‑1 (MQ=255)
                                                                                                                     gTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACt               <  1:65524/143‑1 (MQ=255)
                                                                                                                         aCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAGCGCCGTGCTGAAACCGCGGCAAGAAGTCGCCAAAATgcga           >  1:264200/1‑142 (MQ=255)
                                                                                                                               tacctaaCCTGCTGCTCTTACTGTTTCGTATCAACATCGGTCAGATCCTCGAAACCCACCTTGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCATTGCTGATACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTc     <  2:935420/138‑1 (MQ=255)
                                                                                                                                aCTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCa    <  1:688567/143‑1 (MQ=255)
                                                                                                                                  tGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATc  <  2:106723/143‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                        
GCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATC  >  NC_000913/4184407‑4184679

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A