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
A1 F999 I1 R1 225 156.4 11709729 83.8% 9812752 75.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,941,734 Δ1 bp noncoding (409/2906 nt) rrlC → 23S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,941,7340A.96.7% 92.4 / ‑3.2 30noncoding (409/2906 nt)rrlC23S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base . (16/13);  total (17/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGAGGGACCATCCTCCAAGGCTAAATA  >  NC_000913/3941663‑3941758
                                                                       |                        
gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGAc                     >  1:3082798/1‑76 (MQ=255)
gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGAc                     >  1:5344949/1‑76 (MQ=255)
gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGAc                     <  1:4706735/76‑1 (MQ=255)
gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGAc                     >  1:3604658/1‑76 (MQ=255)
 tACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGCATCCTGTCTGAATATGGG‑GGGAcc                    <  1:1132601/76‑1 (MQ=11)
  acacAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCa                   >  2:5319468/1‑76 (MQ=255)
   cacaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAt                  >  2:3010828/1‑76 (MQ=255)
   cacaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAt                  <  2:4011404/76‑1 (MQ=9)
   cacaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAt                  <  1:4254036/76‑1 (MQ=255)
    acaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtc                 <  2:130343/76‑1 (MQ=9)
    acaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtc                 <  1:3379268/76‑1 (MQ=255)
     caAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcc                >  2:4397010/1‑76 (MQ=255)
     caAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcc                >  1:5207622/1‑76 (MQ=255)
      aaaaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcct               >  1:3846884/1‑76 (MQ=255)
       gaaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctc              >  2:5189822/2‑76 (MQ=255)
       aaaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctc              >  1:731010/1‑76 (MQ=255)
        aaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctcc             <  2:4924875/76‑1 (MQ=12)
        aaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctcc             >  1:1442883/1‑76 (MQ=255)
        aaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctcc             <  2:1678334/76‑1 (MQ=12)
        aaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctcc             >  1:3558045/1‑76 (MQ=255)
          aTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCaa           <  2:1733774/76‑1 (MQ=9)
          aTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCaa           >  1:4377473/1‑76 (MQ=255)
          aTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCCCCaa           >  2:201327/1‑76 (MQ=11)
           tGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAg          >  1:3807770/1‑76 (MQ=255)
            gCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAgg         <  1:2542671/76‑1 (MQ=255)
             cacaTATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAGGc        <  2:2809045/76‑1 (MQ=9)
             cacaTATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAGGc        >  1:5384854/1‑76 (MQ=12)
              acaTATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAGGCt       <  2:1820976/76‑1 (MQ=9)
               caTATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAGGCTa      <  1:3576780/76‑1 (MQ=0)
                   ttGTGAGCTCGATGAGTAGGGCGGGCAACGTGGCATCCTGTCCGACTATGCGAGCAACC‑TCCCCCAACGATAAATa  >  2:267044/1‑76 (MQ=2)
                                                                       |                        
GTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGAGGGACCATCCTCCAAGGCTAAATA  >  NC_000913/3941663‑3941758

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A