BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238284.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 = 3,088,119 number of mapped reads = 2,811,834 (91.05%) number of supplementary alignments = 24,805 (0.8%) number of secondary alignments = 0 number of mapped bases = 186,365,100 bp number of sequenced bases = 186,270,262 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,484 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.885 >>>>>>> ACTG content number of A's = 51,329,346 bp (27.56%) number of C's = 36,101,821 bp (19.38%) number of T's = 56,601,825 bp (30.39%) number of G's = 42,190,583 bp (22.65%) number of N's = 46,687 bp (0.03%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,591,426 number of insertions = 14,884 mapped reads with insertion percentage = 0.52% number of deletions = 57,342 mapped reads with deletion percentage = 2.01% homopolymer indels = 45.33% >>>>>>> Coverage mean coverageData = 0.0602X std coverageData = 0.4636X There is a 4.99% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13920046 0.05584758803870744 0.7577010391669291 chr2 243199373 15908559 0.06541365137483311 0.6040317187963132 chr3 198022430 11887699 0.060032083234207355 0.28408649771726907 chr4 191154276 12246983 0.06406857987314916 0.3161691701278746 chr5 180915260 12299201 0.0679832149040385 0.3044477660999732 chr6 171115067 11017001 0.0643835823060514 0.3685761319288032 chr7 159138663 10941073 0.06875182179958368 0.6067446468122538 chr8 146364022 9496767 0.06488457252151762 0.5616332245740797 chr9 141213431 7896261 0.05591720946147113 0.4678400313699566 chr10 135534747 8947523 0.06601645111714415 0.45090399136322423 chr11 135006516 8370424 0.062000148200254276 0.4100610653247039 chr12 133851895 8739481 0.06529217236707781 0.3093025221685131 chr13 115169878 5420546 0.04706565721985049 0.2528139413415127 chr14 107349540 5858907 0.05457784914588362 0.3238614507733148 chr15 102531392 5250874 0.051212354553813136 0.27242237533285574 chr16 90354753 5523421 0.06113038679879962 0.3331145209328352 chr17 81195210 5282896 0.06506413370936537 0.34910130247823845 chr18 78077248 4567752 0.0585029841215715 0.8700418987589402 chr19 59128983 3778190 0.06389742911695268 0.5945390630376022 chr20 63025520 3635619 0.05768487114426029 0.2950281860949748 chr21 48129895 2152410 0.044720853847696945 0.28440594105696504 chr22 51304566 1984675 0.03868417871422984 0.22728227916484953 chrMT 16571 11691 0.7055096252489289 1.0092013190233022 chrX 155270560 10738340 0.06915889270960315 0.3525845607894439 chrY 59373566 488761 0.008231963025431216 0.17425222332247764