BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975341.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 = 4,616,820 number of mapped reads = 4,450,809 (96.4%) number of supplementary alignments = 21,621 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,223,883 number of mapped paired reads (second in pair) = 2,226,926 number of mapped paired reads (both in pair) = 4,427,142 number of mapped paired reads (singletons) = 23,667 number of mapped bases = 405,697,237 bp number of sequenced bases = 405,450,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 269,713 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 111,471.7788 std insert size = 3,266,641.114 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 52.7098 >>>>>>> ACTG content number of A's = 117,876,883 bp (29.07%) number of C's = 78,450,854 bp (19.35%) number of T's = 120,491,960 bp (29.72%) number of G's = 88,622,431 bp (21.86%) number of N's = 8,317 bp (0%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 3,196,697 number of insertions = 65,818 mapped reads with insertion percentage = 1.44% number of deletions = 139,190 mapped reads with deletion percentage = 3.06% homopolymer indels = 45.9% >>>>>>> Coverage mean coverageData = 0.1311X std coverageData = 1.484X There is a 8.71% of reference with a coverageData >= 1X There is a 2.71% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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 0.01% 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% 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 32508159 0.13042358277614882 2.0562492902221603 chr2 243199373 37238266 0.15311826482381596 1.757829670452742 chr3 198022430 27895472 0.1408702640402908 0.508923447924073 chr4 191154276 26483059 0.1385428542545394 1.0870943309101888 chr5 180915260 25045287 0.13843656416821887 0.5117607532726987 chr6 171115067 25270083 0.14767888908344934 1.666005557768021 chr7 159138663 22305638 0.14016479452262334 1.7320694558406589 chr8 146364022 19056244 0.13019759733030567 0.6585885060814907 chr9 141213431 17879244 0.12661149774060798 2.306041637006962 chr10 135534747 21916205 0.1617017442766909 2.8973680729742086 chr11 135006516 19485042 0.14432667827677295 1.171592847327163 chr12 133851895 18236167 0.13624138081870263 0.4937015350377745 chr13 115169878 12273614 0.106569653568618 0.4259727820493285 chr14 107349540 12167108 0.1133410352759779 0.5112579951760469 chr15 102531392 11641107 0.11353700337941379 0.4481921874932304 chr16 90354753 12990384 0.14377089825036654 1.620748712501305 chr17 81195210 10533542 0.12973107650069504 2.2324919919538595 chr18 78077248 11278471 0.1444527220016771 2.4279373611028605 chr19 59128983 5629471 0.09520662650328351 1.032563674762783 chr20 63025520 8694141 0.1379463588717713 0.561871722994501 chr21 48129895 4982656 0.10352517910126337 0.632891165789288 chr22 51304566 4167528 0.08123113252726863 0.430553008774453 chrMT 16571 148789 8.978878764105968 5.636418420474208 chrX 155270560 13122610 0.08451447589291879 0.6344163553267924 chrY 59373566 4748950 0.07998424753534258 1.9088175758234673