BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536760.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 24,281,356 number of mapped reads = 23,711,124 (97.65%) number of supplementary alignments = 694 (0%) number of secondary alignments = 0 number of mapped bases = 1,182,779,163 bp number of sequenced bases = 1,182,674,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,099 duplication rate = 1.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6116 >>>>>>> ACTG content number of A's = 367,045,834 bp (31.04%) number of C's = 222,180,036 bp (18.79%) number of T's = 367,253,198 bp (31.05%) number of G's = 226,154,507 bp (19.12%) number of N's = 41,008 bp (0%) GC percentage = 37.91% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 2,228,946 number of insertions = 70,256 mapped reads with insertion percentage = 0.3% number of deletions = 62,952 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.21% >>>>>>> Coverage mean coverageData = 0.3821X std coverageData = 0.7838X There is a 25.95% of reference with a coverageData >= 1X There is a 8.14% of reference with a coverageData >= 2X There is a 2.66% of reference with a coverageData >= 3X There is a 0.91% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.05% 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% 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 90388856 0.3626424505477962 0.7784395109432132 chr2 243199373 103766078 0.4266708286291511 0.8197078952656588 chr3 198022430 89542855 0.45218541657124395 0.8369388384673091 chr4 191154276 104508444 0.5467230249141798 0.9370619090800995 chr5 180915260 81864399 0.45250134786860985 0.8354072381374887 chr6 171115067 77767754 0.45447636706357364 0.8433547069204718 chr7 159138663 67201114 0.4222802475096828 0.8168576208063103 chr8 146364022 68446508 0.467645716923521 0.8622676369665243 chr9 141213431 50719801 0.35917122500904325 0.7589180684689777 chr10 135534747 56056224 0.41359301021161754 0.8032091982647045 chr11 135006516 54489933 0.4036096524407755 0.799781487106388 chr12 133851895 54524411 0.4073488163914302 0.8028920607957437 chr13 115169878 47023237 0.40829458028947463 0.810723014160681 chr14 107349540 36570207 0.34066477602046547 0.7479050902958893 chr15 102531392 29872760 0.2913523304160349 0.6906404407896122 chr16 90354753 20864672 0.23091947359980056 0.5910693706714383 chr17 81195210 17777420 0.21894665953816733 0.5833269828199299 chr18 78077248 36958864 0.4733627906557362 0.8528284531875238 chr19 59128983 8604015 0.14551264986242027 0.453626891344996 chr20 63025520 18587797 0.29492492882248333 0.6791944829727299 chr21 48129895 15777296 0.3278065742715624 0.7546949769959805 chr22 51304566 6177284 0.12040417611173243 0.4195975617665025 chrMT 16571 750 0.04525979120149659 0.23408940396668246 chrX 155270560 39531719 0.2545989336291439 0.6124714116399861 chrY 59373566 5756765 0.0969583838033242 0.3862993032884681