BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004133.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 = 1,804,591 number of mapped reads = 1,489,018 (82.51%) number of supplementary alignments = 19,901 (1.1%) number of secondary alignments = 0 number of mapped bases = 98,260,831 bp number of sequenced bases = 98,223,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,933 duplication rate = 5.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.8966 >>>>>>> ACTG content number of A's = 27,467,616 bp (27.96%) number of C's = 18,220,241 bp (18.55%) number of T's = 30,969,783 bp (31.53%) number of G's = 21,559,094 bp (21.95%) number of N's = 7,081 bp (0.01%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 856,966 number of insertions = 6,938 mapped reads with insertion percentage = 0.46% number of deletions = 22,743 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.2679X There is a 2.36% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 10155674 0.04074482927767711 0.293998859181852 chr2 243199373 3010924 0.012380475997362049 0.24969704070941243 chr3 198022430 9267147 0.04679847126408862 0.27761464190646806 chr4 191154276 9372661 0.04903191911856578 0.28889136750060346 chr5 180915260 9213723 0.050928390451971825 0.2874895408383507 chr6 171115067 5498887 0.03213560965966837 0.23906582515425137 chr7 159138663 7599259 0.04775243713088126 0.3985483019367679 chr8 146364022 9707791 0.06632634760474128 0.4170337394901742 chr9 141213431 4847375 0.03432658611630221 0.27329978709909764 chr10 135534747 4299010 0.03171887722636912 0.2801943087227117 chr11 135006516 5227000 0.03871664979488842 0.26272185031367745 chr12 133851895 1641962 0.012267006006900389 0.14348054424040463 chr13 115169878 1864056 0.016185273722352993 0.1638669987890861 chr14 107349540 1278169 0.011906609008291979 0.15075291884917724 chr15 102531392 4312626 0.04206151809584327 0.2629747582039528 chr16 90354753 418480 0.004631521708658758 0.10571864705625074 chr17 81195210 443463 0.005461689180925821 0.09233285454076842 chr18 78077248 1161124 0.014871477027469 0.3322509039009257 chr19 59128983 410332 0.006939608617993649 0.1782281645996716 chr20 63025520 1053013 0.01670772410921798 0.17505699717771783 chr21 48129895 275340 0.005720768765441936 0.11131838226540698 chr22 51304566 221745 0.004322129925044099 0.07779953942891396 chrMT 16571 228406 13.78347715889204 10.33971586541573 chrX 155270560 6536293 0.04209615138890463 0.27389660671264743 chrY 59373566 216371 0.003644231171831586 0.08522040647143256