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 I1 R1 30 31.1 1326154 90.1% 1194864 128.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,184,543 C→A 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_0009134,184,5430CA97.3% 91.0 / NA 39P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (20/16);  total (20/19)
Fisher's exact test for biased strand distribution p-value = 4.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAAC  >  NC_000913/4184422‑4184665
                                                                                                                         |                                                                                                                          
attcAGCCTGTGGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATTCCTTACGATTATATCGGTTCGCCGGTAGACATCGTACTGAACCAGCTGGGc                                                                                                                     <  1:333327/126‑1 (MQ=255)
aTCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCTTTACGTTGAAAACGGTAAGCCGGTAGACATCGTACTGAACCAGCTGGGc                                                                                                                     <  1:530959/129‑1 (MQ=255)
  ccAGCCTGGTGACACGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGt                                                                                                                   <  2:61259/129‑1 (MQ=255)
  ccAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTACAAAACGCAACCAGATCGAAGATATGACATACACTTACAGCGATACGCGGATTGGCAACGTACTGAACCAGCTGGGCga                                                                                                                   >  2:355548/1‑128 (MQ=255)
   cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGAGAGTAATATATAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTa                                                                                                                  >  1:479802/1‑129 (MQ=255)
          ttGACAAGATGGCAGGTCGTCACGGTAACAAGTGTGTAATTTCTCAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                           <  2:484855/128‑1 (MQ=255)
          gttaCAAGATGGTAGCTCGTCACGGTAACAATGGTGTAATTTCTAGGAGCATCCCTATCGAAGTTATTCCTTACGCTGAAAACGGTACGCCGGTAGACATTGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                           <  2:138373/126‑1 (MQ=255)
            gACAAGATGGCAGGTCGTCACGGTCACAAGGGTGTAATTTATAAGATCAACACGATCGAAGATAAGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGAGCGTGCCGTCTCGt                                                                                                         >  1:258200/1‑129 (MQ=255)
                 gATGGCAGGTCGTCACGGTAACAAGGGTGTAATTAATAAGAACAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                    >  1:337921/1‑129 (MQ=255)
                  aTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAAc                                                                                                   >  2:579176/1‑129 (MQ=255)
                       aGGTCGTCACGGTAACAAAGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCgg                                                                                              >  1:546773/1‑129 (MQ=255)
                          tcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                           >  2:533320/1‑129 (MQ=255)
                           cgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTAAGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAg                                                                                          >  1:82668/1‑129 (MQ=255)
                             tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAt                                                                                        >  2:152328/1‑129 (MQ=255)
                             tcACGGTAACAAGAGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAt                                                                                        >  2:98340/1‑129 (MQ=255)
                                  gTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGACAGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACACCGGTCAGATCCTCg                                                                                   >  1:631243/1‑129 (MQ=255)
                                      acgtggTGTAAGTTCTGCGCACAACCCAATCGACGATATGCGTTACGATGAAAACGGTACGCCGGTAGGCAGCGGACTGAACCAGCTGGGCGTACCTGCTCTTATGAACATCGGTCAGATCCTCGAAAc                                                                               <  2:166351/125‑1 (MQ=255)
                                       aaGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAATGTCTCCTCTGAACATCGGTCAGATCCCCGACAcc                                                                              >  2:249772/1‑129 (MQ=255)
                                          ggTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAATCGGTACGCCGGTAGACTTCGTACTGTTCTTGTTGGTTGTACTGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAc                                                                           <  1:366262/129‑1 (MQ=255)
                                             gtAATTTCTAAGATCAACCCGATCGAAGATATACCTTACGATGAAAACGAAACGCCGAAAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACACACCTg                                                                        >  1:218507/1‑129 (MQ=255)
                                             gtAAATTCTAAGATCAAGCCGATCGAAGATATGCCTTACGATGCAAACGGTACGCCGGTAGACATCGTACTGAACAAGCTGGGCGAACCGTCTAGTACGAACATCGGTCAGACCCGCGAAACCCAcccg                                                                        >  2:123738/1‑127 (MQ=255)
                                               aaTTTCTTAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGATATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTggg                                                                      <  2:198997/129‑1 (MQ=255)
                                               aaTGTCTAAGATCAAACCGATCGAAGATATGCCTTAAGATGAAAACGGTTCGTCGAAAGACATCGTACTGATCCATCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAGCCGCGAAACCCACCTggg                                                                      <  1:654843/129‑1 (MQ=255)
                                                aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGTTGTACCTTCTTTTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGt                                                                     <  1:284396/129‑1 (MQ=255)
                                                aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGTGTATTGTCTCGTATGAACATCGGTCAGATCCGCGAAACCCACCTGGGt                                                                     <  1:382328/129‑1 (MQ=255)
                                                aTTTCTAACATCAACCCGATCGAATCTATGCCTGACGATGAAAACGTTACGCCGGTAGACATCGTACTGATCCAGCTTGGCGTATCGTCTCTTATGAACATCAGTCAGATCCGCGAAACCCACCTGGGt                                                                     <  1:470919/129‑1 (MQ=255)
                                                      aaGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATAGTACTGAACCAGCTGAGCGTACCGCCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCt                                                               >  2:96628/1‑129 (MQ=255)
                                                          tCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACAAAAATAGACATCATACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTAAGATCCTCGAAACCCACCTGGGTATGGCTGCGa                                                           >  1:4208/1‑129 (MQ=255)
                                                            aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                         <  2:546773/129‑1 (MQ=255)
                                                            aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCAGGTAAACATCGTACTGAACCAGCCGGGCGTACCCTCTCGTATGAACATCGGTCAGATCCTCGAAACCCCCCTGGGTATGGCTGCGaca                                                         >  1:460227/1‑127 (MQ=255)
                                                                             gtcTTACGATGAAAACGGTACGCCGGTAGACATCCTACTGAGCTAGCTGTTCGTACCGTCTCGTATGATTATCTGTCAGTTTTTTGTTTTCTACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAt                                        <  1:376496/127‑1 (MQ=255)
                                                                               cTTTCGATGAAACCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATTCTTGAAACTCACTTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCa                                      <  1:529276/129‑1 (MQ=255)
                                                                                  aCGATGAAACCGGTAAGCATCTATCTACCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACg                                   <  2:272083/129‑1 (MQ=255)
                                                                                    gATGAAAGCGGTACGCCGGTAGACATCCTACTGCACCGGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAACCCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGcc                                 <  2:436563/129‑1 (MQ=255)
                                                                                          aaCGGTACGCCGGTAGTCATCGTTCTAAACAAACATTGCATAAAATCACATATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTg                           >  1:298452/1‑129 (MQ=255)
                                                                                               tACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCTTTTTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAca                      <  1:579176/129‑1 (MQ=255)
                                                                                                       tAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATAGATCAGATACTCGAAAACCACCTGGGTATGGCTGCGAAAGGTATCGGCGTCAAGATCAACGCCATGCTGAAACAGCAGCaag              >  1:96543/1‑129 (MQ=255)
                                                                                                              cGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcgc       >  2:589500/1‑129 (MQ=255)
                                                                                                                   tGAGCCCGCTGGGCGGTCCTGCTCGCATGATCCTCTGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGGCGCGTAAc  <  2:159804/129‑1 (MQ=255)
                                                                                                                         |                                                                                                                          
ATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAAC  >  NC_000913/4184422‑4184665

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