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
A13 F87 I0 R1 87 48.8 1893308 89.3% 1690724 142.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,159,126 G→A 12.5% A213T (GCG→ACG)  oxyR → DNA‑binding transcriptional dual regulator OxyR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,159,1260GA12.5% 90.8 / 4.1 40A213T (GCG→ACG) oxyRDNA‑binding transcriptional dual regulator OxyR
Reads supporting (aligned to +/- strand):  ref base G (18/17);  new base A (3/2);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

TTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTG  >  NC_000913/4158985‑4159265
                                                                                                                                              |                                                                                                                                           
ttGCTGGTTATCTATGAAGTTCACCCGTTGGGGAACCGCGAATGCGTACGGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGc                                                                                                                                            <  2:184373/143‑1 (MQ=255)
        catctatGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAg                                                                                                                                    <  1:249114/142‑1 (MQ=255)
             atGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATaca                                                                                                                               >  1:891061/1‑143 (MQ=255)
                aaGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGTGCGGATGTAGATacacac                                                                                                                            >  1:268787/1‑143 (MQ=255)
                aaGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATacccac                                                                                                                            >  1:329759/1‑143 (MQ=255)
                            gggCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGAcc                                                                                                                <  1:661344/143‑1 (MQ=255)
                                gAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACCCTTCCGCGCGACCAGcc                                                                                                            >  1:368851/1‑143 (MQ=255)
                                     gcgAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAAGGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCCGCCTGGag                                                                                                       >  1:859496/1‑142 (MQ=255)
                                             gTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTgcg                                                                                               <  1:478670/143‑1 (MQ=255)
                                               aCCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCa                                                                                             >  2:265584/1‑143 (MQ=255)
                                                 cggtGGCCGCTCTTGCAGGGGAAAATCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGTCAATTGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAAc                                                                                           <  2:899292/140‑1 (MQ=255)
                                                     ggCCGATCTGTCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACAtgg                                                                                       <  2:724185/143‑1 (MQ=255)
                                                        cGATCTGGGAGGGGAAAATCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACAtggtgg                                                                                    <  2:180417/143‑1 (MQ=255)
                                                              ggCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAg                                                                              <  1:585384/143‑1 (MQ=255)
                                                                 aGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGCTACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCACCATGGTGGCGGCAGGTa                                                                           >  1:822885/1‑143 (MQ=255)
                                                                           tggctgAGGCTGGGAGATGGTCAGTGGTTGCGCGATCGTGCAATGGGGTTCTGT‑TTGGAAGCCGGCGCGGATGAATATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCAc                                                                 <  2:470398/141‑1 (MQ=255)
                                                                           ctgctgATGCTGGAAGATGGTCACTGTGTGCGCGATCAGGCAATGGGTCTCCGTCATAGTAG‑CGGTGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCAc                                                                 <  1:937429/143‑1 (MQ=255)
                                                                           ctgccgAGGCTGGCAGATGGTCACTGTTGGCGCGATCAGGCAATGGGTTTCTGT‑TGTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCAc                                                                 <  2:476524/143‑1 (MQ=255)
                                                                             gcggATGCTGGAGGATGGTCGCGGTTTGGGCGATCAGGCAATGGGTTTCTGG‑TTGGAAGCCGGGGCGGATGAAGACACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACtt                                                               <  2:675665/140‑1 (MQ=255)
                                                                                 aTGCTGGAAGATGGTCACTGTTTGCGCGATCAGGGGATGGGTGGCGGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCCCGACCAGCCTGGGACCTCTGCGCCACATGGTGGCGGCAGGTAGCGGGATCACTTTACt                                                           >  2:622845/1‑143 (MQ=255)
                                                                                 aTGCTCGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGACGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACt                                                           <  1:847175/143‑1 (MQ=255)
                                                                                   gCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGAGCACCTTACTGc                                                         >  1:322449/1‑143 (MQ=255)
                                                                                     tGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGGTCACTTTACTGccc                                                       >  2:213712/1‑142 (MQ=255)
                                                                                     tGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCa                                                       >  1:538311/1‑143 (MQ=255)
                                                                                       gAAGATGGTCACTGTCTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGACGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAgc                                                     >  2:793582/1‑143 (MQ=255)
                                                                                         tgATGGTTTCTGTGTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCGGGGGCGGATGAAGATACACACTGCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAgcgc                                                   <  2:319245/142‑1 (MQ=255)
                                                                                            tGGTCACTGTTTGCGCGATCAGGCAATGGGGTTCGGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTGCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCgctgg                                                <  2:241764/143‑1 (MQ=255)
                                                                                                     tttGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGACGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGCAGCGGGCTCACTTTACTGCCACCGCTGGCTGcgccgc                                       >  2:775480/1‑143 (MQ=255)
                                                                                                        gcgcGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCgg                                    <  1:767530/143‑1 (MQ=255)
                                                                                                              tCAGGCGATGGGTGTTTGT‑TTTGAAGCCGGGACGGAGGGAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGTAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCTCa                              <  2:903398/143‑1 (MQ=255)
                                                                                                              tCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAgcgcg                              >  1:633631/1‑142 (MQ=255)
                                                                                                                    aaTGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGGAACTCTGCGCACCATGGTGGCGGCAGGTAGCGGGATCACTTTACGGCCAGCGCTGCCTGTGCCGCCGGAGCGCaagaccg                        >  2:269126/1‑138 (MQ=255)
                                                                                                                    aaTGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCGAAcgcg                        >  1:156831/1‑143 (MQ=255)
                                                                                                                       gggTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGACGCCCGATCGCCAAcgcggtc                     >  2:95050/1‑140 (MQ=255)
                                                                                                                         gTTTCTGT‑TTTGAAGCCGGGACGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACGTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCTAGcgcgccggg                   >  1:69462/1‑138 (MQ=255)
                                                                                                                             cTGT‑TTTGGAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGCGCGCCAACGCGCTGGCgttg               >  2:932560/1‑143 (MQ=255)
                                                                                                                                 ttgtGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACAGGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGttt            <  2:168604/140‑1 (MQ=255)
                                                                                                                                   ttGAGGCCGGGGCGGATGACGATACGCTGTGCCGCGCGACCAGCCCGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTAt          <  1:586502/143‑1 (MQ=255)
                                                                                                                                     gAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGGTGTTGATCt        >  1:742186/1‑143 (MQ=255)
                                                                                                                                        gCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGcc     >  1:237207/1‑143 (MQ=255)
                                                                                                                                           ggggCGGATGAAGTTACACACTTCCGCGCGCCCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTg  <  1:88309/143‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                           
TTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGT‑TTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTG  >  NC_000913/4158985‑4159265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A