BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230354.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,013,673 number of mapped reads = 1,429,195 (70.97%) number of supplementary alignments = 4,094 (0.2%) number of secondary alignments = 0 number of mapped bases = 85,886,409 bp number of sequenced bases = 85,842,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,153 duplication rate = 6.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7178 >>>>>>> ACTG content number of A's = 21,372,165 bp (24.9%) number of C's = 13,576,831 bp (15.82%) number of T's = 29,732,131 bp (34.64%) number of G's = 21,019,630 bp (24.49%) number of N's = 141,313 bp (0.16%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 820,621 number of insertions = 7,101 mapped reads with insertion percentage = 0.49% number of deletions = 29,002 mapped reads with deletion percentage = 2.01% homopolymer indels = 50.48% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2631X There is a 2.24% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 8858329 0.03553984726080181 0.42110437885025354 chr2 243199373 7731703 0.03179162390356985 0.28989176004341993 chr3 198022430 5769548 0.02913583072382255 0.20553139050214275 chr4 191154276 5631617 0.029461109203751217 0.21442610578944576 chr5 180915260 5511493 0.03046450034120947 0.2111782077975336 chr6 171115067 4556846 0.02663030252035024 0.23535608441263098 chr7 159138663 4372105 0.027473556190427465 0.33594087863391026 chr8 146364022 5271467 0.03601613926679331 0.31513344380302477 chr9 141213431 3797218 0.02688992097359351 0.27904353027427603 chr10 135534747 3560075 0.026266880477520647 0.2396164381371887 chr11 135006516 4085277 0.030259850568990315 0.24711997695950375 chr12 133851895 4303342 0.03215002671422769 0.22039995333430762 chr13 115169878 2153399 0.01869758861774604 0.16364161447123202 chr14 107349540 2036663 0.01897225642513233 0.18493011447427143 chr15 102531392 2089346 0.02037762249438689 0.17452424113899617 chr16 90354753 2156982 0.023872368949976543 0.19612934625785206 chr17 81195210 1946520 0.023973335372862514 0.20463126198923115 chr18 78077248 1486614 0.019040297117029533 0.357964143178992 chr19 59128983 1248214 0.021110019768139764 0.31277301996303514 chr20 63025520 1741411 0.027630251999507503 0.20562634735903337 chr21 48129895 1136933 0.023622179105107128 0.19115264057408507 chr22 51304566 890402 0.017355219416533025 0.15495041814142538 chrMT 16571 80370 4.850039225152375 4.556224163486135 chrX 155270560 5257844 0.033862465621300006 0.2474669746422102 chrY 59373566 212691 0.0035822507275375714 0.08578833905479287