BamQC report ----------------------------------- >>>>>>> Input bam file = SRR4012089.sorted.bam outfile = /mainsd/zhouyj/SRP081010/SRP081010.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 = 152,249,128 number of mapped reads = 142,853,692 (93.83%) number of supplementary alignments = 39,571 (0.03%) number of secondary alignments = 0 number of mapped bases = 7,919,425,762 bp number of sequenced bases = 7,917,053,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,652,441 duplication rate = 38.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5403 >>>>>>> ACTG content number of A's = 2,271,926,780 bp (28.7%) number of C's = 1,496,716,223 bp (18.9%) number of T's = 2,367,653,549 bp (29.91%) number of G's = 1,780,687,250 bp (22.49%) number of N's = 69,530 bp (0%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 32,320,135 number of insertions = 562,668 mapped reads with insertion percentage = 0.39% number of deletions = 1,288,057 mapped reads with deletion percentage = 0.9% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 2.5582X std coverageData = 25.4111X There is a 30.56% of reference with a coverageData >= 1X There is a 19.95% of reference with a coverageData >= 2X There is a 14.94% of reference with a coverageData >= 3X There is a 11.98% of reference with a coverageData >= 4X There is a 10% of reference with a coverageData >= 5X There is a 8.58% of reference with a coverageData >= 6X There is a 7.51% of reference with a coverageData >= 7X There is a 6.66% of reference with a coverageData >= 8X There is a 5.98% of reference with a coverageData >= 9X There is a 5.42% of reference with a coverageData >= 10X There is a 4.95% of reference with a coverageData >= 11X There is a 4.55% of reference with a coverageData >= 12X There is a 4.21% of reference with a coverageData >= 13X There is a 3.91% of reference with a coverageData >= 14X There is a 3.64% of reference with a coverageData >= 15X There is a 3.41% of reference with a coverageData >= 16X There is a 3.2% of reference with a coverageData >= 17X There is a 3.01% of reference with a coverageData >= 18X There is a 2.84% of reference with a coverageData >= 19X There is a 2.69% of reference with a coverageData >= 20X There is a 2.55% of reference with a coverageData >= 21X There is a 2.42% of reference with a coverageData >= 22X There is a 2.3% of reference with a coverageData >= 23X There is a 2.19% of reference with a coverageData >= 24X There is a 2.09% of reference with a coverageData >= 25X There is a 1.99% of reference with a coverageData >= 26X There is a 1.91% of reference with a coverageData >= 27X There is a 1.83% of reference with a coverageData >= 28X There is a 1.75% of reference with a coverageData >= 29X There is a 1.68% of reference with a coverageData >= 30X There is a 1.61% of reference with a coverageData >= 31X There is a 1.55% of reference with a coverageData >= 32X There is a 1.49% of reference with a coverageData >= 33X There is a 1.44% of reference with a coverageData >= 34X There is a 1.39% of reference with a coverageData >= 35X There is a 1.34% of reference with a coverageData >= 36X There is a 1.29% of reference with a coverageData >= 37X There is a 1.25% of reference with a coverageData >= 38X There is a 1.2% of reference with a coverageData >= 39X There is a 1.16% of reference with a coverageData >= 40X There is a 1.13% of reference with a coverageData >= 41X There is a 1.09% of reference with a coverageData >= 42X There is a 1.06% of reference with a coverageData >= 43X There is a 1.02% of reference with a coverageData >= 44X There is a 0.99% of reference with a coverageData >= 45X There is a 0.96% of reference with a coverageData >= 46X There is a 0.94% of reference with a coverageData >= 47X There is a 0.91% of reference with a coverageData >= 48X There is a 0.88% of reference with a coverageData >= 49X There is a 0.86% of reference with a coverageData >= 50X There is a 0.84% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 637351039 2.557069011274399 16.35732283321378 chr2 243199373 708240244 2.9121795638839907 50.38102731416322 chr3 198022430 538008850 2.71690863504705 14.957764020303156 chr4 191154276 477382893 2.4973696795566322 17.883339888546296 chr5 180915260 480472344 2.6557867147304215 14.91982994859111 chr6 171115067 470622443 2.7503273162964663 36.595640108875706 chr7 159138663 406958722 2.557258646819221 19.66801493196407 chr8 146364022 406902472 2.7800716763577324 17.903441340104774 chr9 141213431 328950032 2.3294528691112957 25.06717439439544 chr10 135534747 366489467 2.7040259056225633 23.123608124612193 chr11 135006516 353785619 2.6205077316416343 17.253689972079243 chr12 133851895 368416711 2.752420583959607 17.60878453760246 chr13 115169878 242461128 2.1052477627874193 12.452490432977196 chr14 107349540 243062678 2.2642172290631146 21.7361157712164 chr15 102531392 223753936 2.1822968715766584 13.060585295566135 chr16 90354753 225263334 2.4930988854565292 29.131001185522628 chr17 81195210 211133759 2.600322839241379 13.730479669987165 chr18 78077248 206938508 2.650432914848638 27.367024292180552 chr19 59128983 161381911 2.729319917442179 35.766528351935605 chr20 63025520 176350542 2.7980815073005347 35.37670587714882 chr21 48129895 97019364 2.0157817506146647 20.353904591467636 chr22 51304566 93094487 1.8145458437364035 11.136049205489279 chrMT 16571 5229651 315.5905497555971 1191.4118560864933 chrX 155270560 468426550 3.016840732718424 19.6265982013008 chrY 59373566 21729078 0.36597225775524417 38.04459695665823