BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081693.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 = 2,487,632 number of mapped reads = 2,171,704 (87.3%) number of supplementary alignments = 25,939 (1.04%) number of secondary alignments = 0 number of mapped bases = 146,593,876 bp number of sequenced bases = 146,539,671 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,030 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4362 >>>>>>> ACTG content number of A's = 41,271,801 bp (28.16%) number of C's = 26,199,751 bp (17.88%) number of T's = 47,493,811 bp (32.41%) number of G's = 31,467,885 bp (21.47%) number of N's = 106,423 bp (0.07%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,276,507 number of insertions = 12,508 mapped reads with insertion percentage = 0.57% number of deletions = 33,446 mapped reads with deletion percentage = 1.53% homopolymer indels = 49.44% >>>>>>> Coverage mean coverageData = 0.0474X std coverageData = 0.3771X There is a 3.79% of reference with a coverageData >= 1X There is a 0.68% 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% 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 11493114 0.04611067348153167 0.5785563446410501 chr2 243199373 12457165 0.051222027616000476 0.4008893581217732 chr3 198022430 9985329 0.05042524223139773 0.2694188268171641 chr4 191154276 10150151 0.05309926208503962 0.2945079685690817 chr5 180915260 9356844 0.05171948458079213 0.27340522110255333 chr6 171115067 9186590 0.05368662246440286 0.3301296090402204 chr7 159138663 8126924 0.0510681932774564 0.41280464948385376 chr8 146364022 7881832 0.05385088420158336 0.6772676180560595 chr9 141213431 6275738 0.04444150924992397 0.3534513645414975 chr10 135534747 6650026 0.04906510062692632 0.3549805945652421 chr11 135006516 6582844 0.0487594539510967 0.3536519455683877 chr12 133851895 6240805 0.04662470411793572 0.2617454766816673 chr13 115169878 4738528 0.04114381366280513 0.24266740740316237 chr14 107349540 4540216 0.04229376297280827 0.2594552949655582 chr15 102531392 3936911 0.03839712816929278 0.23348309089974548 chr16 90354753 3871110 0.0428434572777815 0.26562800791948943 chr17 81195210 3217256 0.039623716719249816 0.2672874522067111 chr18 78077248 3985075 0.05104015705061736 0.6131058585344009 chr19 59128983 2172324 0.036738734369911284 0.4401453219818639 chr20 63025520 2855387 0.04530525095231265 0.2678686618837789 chr21 48129895 1948503 0.04048425619877209 0.26115149902862145 chr22 51304566 1345581 0.02622731473841919 0.19240690062963975 chrMT 16571 49935 3.013396898195643 2.2726115751147167 chrX 155270560 9182772 0.05914045779186988 0.3152151544336527 chrY 59373566 362916 0.0061124170982083175 0.1574692912280669