BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081253.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,793,656 number of mapped reads = 5,114,692 (88.28%) number of supplementary alignments = 58,926 (1.02%) number of secondary alignments = 0 number of mapped bases = 349,393,155 bp number of sequenced bases = 349,256,207 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 318,300 duplication rate = 4.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5435 >>>>>>> ACTG content number of A's = 98,624,358 bp (28.24%) number of C's = 64,534,621 bp (18.48%) number of T's = 111,061,923 bp (31.8%) number of G's = 74,939,140 bp (21.46%) number of N's = 96,165 bp (0.03%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 2,960,700 number of insertions = 29,043 mapped reads with insertion percentage = 0.56% number of deletions = 84,537 mapped reads with deletion percentage = 1.64% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.1129X std coverageData = 0.7832X There is a 7.96% of reference with a coverageData >= 1X There is a 2.13% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 28687080 0.11509331405035897 1.275771115259367 chr2 243199373 28609658 0.11763869966885153 0.8019896342864798 chr3 198022430 22755691 0.11491471445936706 0.45699161891910817 chr4 191154276 23941819 0.1252486708693872 0.5323317320291207 chr5 180915260 20969855 0.1159098187737176 0.45649210860675626 chr6 171115067 21836683 0.1276140282842539 0.576009699543787 chr7 159138663 19398616 0.12189756803473961 0.8980614391099886 chr8 146364022 17252591 0.1178745347678407 1.4217450276334287 chr9 141213431 14669454 0.10388143603705798 0.7946090711679581 chr10 135534747 16650830 0.12285285042071167 0.9380039136500021 chr11 135006516 14035231 0.10395965628799723 0.7236251756117195 chr12 133851895 15233476 0.11380844477397947 0.4742429157869318 chr13 115169878 10986416 0.09539313743129953 0.408375225835521 chr14 107349540 11661981 0.1086355935945324 0.5345393605941285 chr15 102531392 10594234 0.10332673528903226 0.42545526481278834 chr16 90354753 9802055 0.10848411040424183 0.5213119324348243 chr17 81195210 8492646 0.1045954065516919 0.5633931141112277 chr18 78077248 9005293 0.1153382480898917 1.28062588767295 chr19 59128983 5653438 0.09561196071983853 1.1104095360384667 chr20 63025520 6059194 0.09613873872044214 0.4401944924334226 chr21 48129895 4201109 0.08728689310458708 0.4896150456715102 chr22 51304566 3160218 0.06159720754679028 0.32428789249812445 chrMT 16571 89185 5.381992637740631 3.774211334252067 chrX 155270560 24758789 0.15945578479268704 0.5981813067688616 chrY 59373566 887613 0.014949632636180215 0.3369950339931246