BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818885.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,916,636 number of mapped reads = 1,882,124 (98.2%) number of supplementary alignments = 29,595 (1.54%) number of secondary alignments = 0 number of mapped bases = 174,095,534 bp number of sequenced bases = 173,982,040 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 372,546 duplication rate = 16.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1973 >>>>>>> ACTG content number of A's = 50,626,831 bp (29.1%) number of C's = 37,503,506 bp (21.56%) number of T's = 49,453,648 bp (28.42%) number of G's = 36,395,433 bp (20.92%) number of N's = 2,622 bp (0%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,066,756 number of insertions = 24,335 mapped reads with insertion percentage = 1.25% number of deletions = 57,693 mapped reads with deletion percentage = 2.99% homopolymer indels = 41.05% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.6961X There is a 4.02% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 15983756 0.06412724644726162 1.0898958356390815 chr2 243199373 11105766 0.04566527398078448 1.0011956455593949 chr3 198022430 10325554 0.0521433556794551 0.29613225994554426 chr4 191154276 10307581 0.05392283769786034 0.40770084684399555 chr5 180915260 9218971 0.050957398508008664 0.31813597306336167 chr6 171115067 7710549 0.04506060825140547 0.3188707259376821 chr7 159138663 15065621 0.09466977236072419 1.4812386147171936 chr8 146364022 17068449 0.11661642503920806 0.5878250491574383 chr9 141213431 6219462 0.044042991916257594 0.5404339705402786 chr10 135534747 7752141 0.05719670543229774 0.9351472145621142 chr11 135006516 7341208 0.054376693936757835 0.3946755770786739 chr12 133851895 6578710 0.049149173420368834 0.2906691830988138 chr13 115169878 4242231 0.036834553215381545 0.24633936079636473 chr14 107349540 5690771 0.053011601167550416 0.336027468127646 chr15 102531392 4645029 0.045303481298683626 0.2738608716852165 chr16 90354753 4245617 0.046988308406974454 0.7764887819620899 chr17 81195210 4499831 0.055419907159547956 0.42020986633702656 chr18 78077248 2992050 0.03832166318157115 0.6210616213780306 chr19 59128983 3303044 0.055861674468508954 0.9981494064131887 chr20 63025520 6812945 0.10809819577847196 0.4686392855663486 chr21 48129895 2048479 0.042561468293251005 0.3179689618835675 chr22 51304566 2025414 0.03947824059168535 0.29981861495862183 chrMT 16571 269866 16.28543841651077 10.584502648790911 chrX 155270560 7948773 0.05119304651184359 0.3727419720294884 chrY 59373566 693716 0.011683920079855066 0.8847722117190602