BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084257.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 = 1,242,562 number of mapped reads = 1,001,874 (80.63%) number of supplementary alignments = 6,734 (0.54%) number of secondary alignments = 0 number of mapped bases = 69,160,821 bp number of sequenced bases = 69,136,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,297 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7575 >>>>>>> ACTG content number of A's = 21,420,244 bp (30.98%) number of C's = 12,551,656 bp (18.15%) number of T's = 20,783,070 bp (30.06%) number of G's = 14,380,764 bp (20.8%) number of N's = 810 bp (0%) GC percentage = 38.96% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 614,165 number of insertions = 5,395 mapped reads with insertion percentage = 0.53% number of deletions = 15,501 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.85% >>>>>>> Coverage mean coverageData = 0.0223X std coverageData = 0.1912X There is a 2.08% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6673844 0.02677563639851473 0.3012266060952494 chr2 243199373 6634568 0.027280366384826164 0.20178683206715028 chr3 198022430 4777934 0.024128246481976815 0.1652943244016337 chr4 191154276 3255466 0.017030568544540433 0.1380941495963302 chr5 180915260 3535354 0.019541491414267653 0.14707098593184914 chr6 171115067 3266657 0.01909041124940798 0.15459017084023977 chr7 159138663 3992301 0.025086933148357544 0.24645407963666255 chr8 146364022 3477313 0.023757976533331397 0.21225558651175708 chr9 141213431 2633855 0.01865158987603665 0.15948374655000994 chr10 135534747 4544638 0.03353116525904608 0.24389803866157042 chr11 135006516 3999141 0.029621836919338028 0.20023840437556717 chr12 133851895 3275603 0.02447184628951275 0.16442590545217114 chr13 115169878 1885421 0.016370782297781022 0.13386831893527065 chr14 107349540 1967097 0.018324223839245143 0.14432295786780114 chr15 102531392 1584680 0.015455559210587914 0.13077779319883287 chr16 90354753 1414084 0.015650355438412852 0.13832778600074822 chr17 81195210 1730308 0.021310468930371633 0.1602409545796509 chr18 78077248 1900388 0.024339843535468874 0.25172651424401105 chr19 59128983 1325137 0.022410955385449467 0.21160287451555485 chr20 63025520 1316093 0.020881906250039665 0.15263245331145547 chr21 48129895 648411 0.013472105019136236 0.12433504479195258 chr22 51304566 544515 0.010613382832241482 0.10802541946996386 chrMT 16571 52935 3.1944360630016293 2.7391633013446195 chrX 155270560 4593387 0.02958311607815416 0.19300848425098924 chrY 59373566 131691 0.002218007252587793 0.055320345212258405