BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818800.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 = 1,359,749 number of mapped reads = 1,322,186 (97.24%) number of supplementary alignments = 11,397 (0.84%) number of secondary alignments = 0 number of mapped bases = 89,700,655 bp number of sequenced bases = 89,664,731 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 539,859 duplication rate = 34.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8943 >>>>>>> ACTG content number of A's = 26,083,944 bp (29.09%) number of C's = 20,464,246 bp (22.82%) number of T's = 24,635,713 bp (27.48%) number of G's = 18,475,275 bp (20.6%) number of N's = 5,553 bp (0.01%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 465,218 number of insertions = 8,151 mapped reads with insertion percentage = 0.61% number of deletions = 22,392 mapped reads with deletion percentage = 1.68% homopolymer indels = 44.44% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.3817X There is a 1.5% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 7413725 0.0297440582906311 0.5280753828764961 chr2 243199373 7954333 0.03270704567153633 0.599261759868538 chr3 198022430 6122781 0.03091963370008135 0.30282998436291214 chr4 191154276 5888423 0.03080455809421705 0.3330360200154782 chr5 180915260 5543602 0.030641981223695557 0.30556985987151364 chr6 171115067 5305379 0.031004744894849032 0.32309589351783136 chr7 159138663 4851434 0.030485577222676554 0.34938158572287126 chr8 146364022 4620356 0.03156756651576574 0.33345048838808505 chr9 141213431 3884707 0.0275094725231908 0.32851883664345083 chr10 135534747 4347383 0.032075782013301725 0.3963880834419785 chr11 135006516 4247567 0.031461940696254985 0.33355733177055596 chr12 133851895 4123639 0.03080747568048999 0.3350860658849946 chr13 115169878 2880754 0.02501308545277785 0.27065236256020486 chr14 107349540 2778234 0.025880259943358862 0.3162080342909258 chr15 102531392 2614447 0.025498990592071547 0.27646122133684686 chr16 90354753 2584949 0.0286088879021118 0.40016296343552454 chr17 81195210 2361601 0.029085471913922016 0.30660041876692473 chr18 78077248 2471285 0.03165179438701528 0.4033261428430034 chr19 59128983 1769743 0.02993021205861092 0.45113225795379985 chr20 63025520 1925111 0.030544944333660395 0.3190242924014642 chr21 48129895 1196946 0.02486907565453862 0.2835865242597882 chr22 51304566 1099584 0.021432478349003088 0.28247040302801985 chrMT 16571 91092 5.49707320016897 5.853678891354812 chrX 155270560 2751702 0.017721981552716756 0.24016237395988868 chrY 59373566 871878 0.014684615709287193 0.5743779216837569