BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975325.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,069,676 number of mapped reads = 4,013,006 (98.61%) number of supplementary alignments = 32,378 (0.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,005,295 number of mapped paired reads (second in pair) = 2,007,711 number of mapped paired reads (both in pair) = 3,989,906 number of mapped paired reads (singletons) = 23,100 number of mapped bases = 375,360,569 bp number of sequenced bases = 375,087,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 441,487 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 112,990.2542 std insert size = 3,178,699.6728 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 52.1508 >>>>>>> ACTG content number of A's = 109,575,654 bp (29.21%) number of C's = 74,818,486 bp (19.95%) number of T's = 110,537,638 bp (29.47%) number of G's = 80,147,530 bp (21.37%) number of N's = 7,751 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 3,493,092 number of insertions = 75,655 mapped reads with insertion percentage = 1.82% number of deletions = 136,198 mapped reads with deletion percentage = 3.28% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.1213X std coverageData = 3.4615X There is a 7.9% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 34117883 0.1368818374980097 2.4563469185767164 chr2 243199373 21436052 0.08814188842501662 2.4034073799762643 chr3 198022430 22006471 0.11113120367223046 0.9587711495972162 chr4 191154276 23592563 0.12342158121537392 2.889382950347264 chr5 180915260 22549933 0.12464362044417923 0.5041830927630776 chr6 171115067 21448521 0.12534560150685037 1.7119473657612314 chr7 159138663 17578287 0.1104589335402422 2.218033779784442 chr8 146364022 21667967 0.14804162050151914 0.7817283800628426 chr9 141213431 13777789 0.09756712872446248 2.193498188357883 chr10 135534747 27179980 0.20053883304183243 14.205354367606315 chr11 135006516 15685237 0.11618133305506528 1.8193520715116704 chr12 133851895 18641713 0.13927119223825707 0.4926930252206857 chr13 115169878 8225100 0.07141711133878252 0.33425867406082943 chr14 107349540 21748031 0.20259081687727773 0.6668491087297266 chr15 102531392 6004047 0.058558134078585414 0.30431627273251893 chr16 90354753 10142594 0.11225302115540065 2.7974960941401754 chr17 81195210 10073808 0.12406899372512245 2.090921688962252 chr18 78077248 17206445 0.22037719618396387 2.7905703402377213 chr19 59128983 4669122 0.07896503141276758 1.4643634712739502 chr20 63025520 6906117 0.10957651757573758 0.7850404069464544 chr21 48129895 5475425 0.11376349356257685 1.030488549008991 chr22 51304566 3378337 0.0658486615012005 0.387306156429348 chrMT 16571 55819 3.368475046768451 2.818916623072877 chrX 155270560 19714352 0.12696773940919645 0.8918413391302611 chrY 59373566 2078976 0.0350151783034221 2.5482118868282715