BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975335.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 = 4,716,378 number of mapped reads = 4,613,542 (97.82%) number of supplementary alignments = 28,043 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,305,063 number of mapped paired reads (second in pair) = 2,308,479 number of mapped paired reads (both in pair) = 4,577,276 number of mapped paired reads (singletons) = 36,266 number of mapped bases = 420,368,996 bp number of sequenced bases = 420,101,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 318,036 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 86,392.2814 std insert size = 2,771,180.0894 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 52.588 >>>>>>> ACTG content number of A's = 125,318,522 bp (29.83%) number of C's = 79,578,502 bp (18.94%) number of T's = 126,966,846 bp (30.22%) number of G's = 88,229,144 bp (21%) number of N's = 8,800 bp (0%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 3,301,583 number of insertions = 83,801 mapped reads with insertion percentage = 1.76% number of deletions = 139,950 mapped reads with deletion percentage = 2.96% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.1358X std coverageData = 1.8189X There is a 9.24% of reference with a coverageData >= 1X There is a 2.62% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% 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% 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 31653210 0.12699350506332338 1.9877603800664387 chr2 243199373 37932114 0.15597126560026123 2.362922858800651 chr3 198022430 24845754 0.125469392532957 0.480469155726695 chr4 191154276 29420064 0.15390743338642343 1.7859416749239083 chr5 180915260 25675997 0.14192278196985705 0.532078045825569 chr6 171115067 36936064 0.21585512396754636 2.457845845642512 chr7 159138663 21945195 0.1378998326761109 1.7838168669759449 chr8 146364022 21259480 0.14525072288598356 0.7517538938233489 chr9 141213431 17607871 0.12468977543644556 2.777788191282016 chr10 135534747 22018664 0.1624577054030285 3.846241792895684 chr11 135006516 18936488 0.14026351142932983 1.179174711323463 chr12 133851895 17712310 0.13232767455402855 0.47671304506420137 chr13 115169878 13059042 0.1133893881523431 0.46880790093755864 chr14 107349540 12240160 0.11402154121945934 0.5457497383474589 chr15 102531392 10747024 0.10481691304844472 0.4126353935941629 chr16 90354753 12366919 0.13687070784201025 2.0120159547307 chr17 81195210 8306665 0.10230486502836805 1.9323783119862514 chr18 78077248 17096438 0.21896824539717383 3.0204252747456195 chr19 59128983 4817971 0.08148239248424076 1.1437105250801114 chr20 63025520 7750481 0.12297369383068954 0.6007045365857584 chr21 48129895 5287558 0.10986016071715926 0.7612085783367362 chr22 51304566 3325046 0.06480994303703885 0.4091431544651293 chrMT 16571 170993 10.318809969223341 51.1759449222379 chrX 155270560 13088709 0.08429614087821928 0.607404618591712 chrY 59373566 6168779 0.10389773455749651 3.0675322849669455