BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124962.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,924,774 number of mapped reads = 2,855,406 (97.63%) number of supplementary alignments = 69,911 (2.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,438,656 number of mapped paired reads (second in pair) = 1,416,750 number of mapped paired reads (both in pair) = 2,830,396 number of mapped paired reads (singletons) = 25,010 number of mapped bases = 358,033,856 bp number of sequenced bases = 357,653,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 548,514 duplication rate = 16.66% >>>>>>> Insert size mean insert size = 93,298.7548 std insert size = 2,922,009.9111 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 53.4147 >>>>>>> ACTG content number of A's = 102,631,278 bp (28.7%) number of C's = 71,780,961 bp (20.07%) number of T's = 104,027,145 bp (29.09%) number of G's = 79,211,568 bp (22.15%) number of N's = 2,665 bp (0%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 3,982,888 number of insertions = 90,986 mapped reads with insertion percentage = 2.93% number of deletions = 167,917 mapped reads with deletion percentage = 5.59% homopolymer indels = 44.39% >>>>>>> Coverage mean coverageData = 0.1157X std coverageData = 1.9093X There is a 6.53% of reference with a coverageData >= 1X There is a 3.13% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% 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 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 29107595 0.116780431211042 0.816257357191819 chr2 243199373 33143632 0.13628173293029008 2.044707389792064 chr3 198022430 24984351 0.12616929809416033 0.5488722172798475 chr4 191154276 23596353 0.1234414081325599 2.7500815348289738 chr5 180915260 21211548 0.11724576467457748 0.5091930086489095 chr6 171115067 22961090 0.1341850861093372 0.6557018219176287 chr7 159138663 22666907 0.14243494681113414 0.8699975309062976 chr8 146364022 18929135 0.12932915303461667 0.5641715772915473 chr9 141213431 14424430 0.10214630363311547 1.087105933248798 chr10 135534747 19881790 0.14669146060382582 6.618236733332715 chr11 135006516 12267011 0.09086236252478362 0.5468426341156216 chr12 133851895 14625043 0.10926287595704193 0.47253143322563707 chr13 115169878 7921647 0.06878228176989126 0.3710640683097215 chr14 107349540 11372187 0.10593605710839563 0.49946082545282194 chr15 102531392 9443526 0.09210375296572586 0.43426002329161634 chr16 90354753 13428282 0.14861732840993988 2.6438519092991286 chr17 81195210 9201328 0.11332353226255588 0.8950177692769588 chr18 78077248 6733826 0.08624568837262298 1.1227003935692972 chr19 59128983 7267800 0.12291434134762642 0.652735773129949 chr20 63025520 7812823 0.12396284870001865 1.0627874032683189 chr21 48129895 3940460 0.08187136082470158 1.4892358629202886 chr22 51304566 3726194 0.07262889622728706 0.4275097511363118 chrMT 16571 1392836 84.05262205057028 43.212685482737236 chrX 155270560 11343467 0.07305613504581937 0.4264798352056388 chrY 59373566 6650595 0.11201272633683482 3.868236001673293