BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153319.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 56,906,248 number of mapped reads = 56,437,707 (99.18%) number of supplementary alignments = 281,461 (0.49%) number of secondary alignments = 0 number of mapped bases = 5,498,130,276 bp number of sequenced bases = 5,497,446,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,020,101 duplication rate = 60.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.6271 >>>>>>> ACTG content number of A's = 1,451,943,582 bp (26.41%) number of C's = 1,287,936,953 bp (23.43%) number of T's = 1,492,983,546 bp (27.16%) number of G's = 1,262,774,224 bp (22.97%) number of N's = 1,808,155 bp (0.03%) GC percentage = 46.4% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 15,286,396 number of insertions = 381,696 mapped reads with insertion percentage = 0.67% number of deletions = 337,090 mapped reads with deletion percentage = 0.59% homopolymer indels = 49.57% >>>>>>> Coverage mean coverageData = 1.7761X std coverageData = 19.288X There is a 10.85% of reference with a coverageData >= 1X There is a 7.64% of reference with a coverageData >= 2X There is a 5.24% of reference with a coverageData >= 3X There is a 4.38% of reference with a coverageData >= 4X There is a 3.5% of reference with a coverageData >= 5X There is a 3.2% of reference with a coverageData >= 6X There is a 2.82% of reference with a coverageData >= 7X There is a 2.65% of reference with a coverageData >= 8X There is a 2.45% of reference with a coverageData >= 9X There is a 2.34% of reference with a coverageData >= 10X There is a 2.22% of reference with a coverageData >= 11X There is a 2.13% of reference with a coverageData >= 12X There is a 2.04% of reference with a coverageData >= 13X There is a 1.97% of reference with a coverageData >= 14X There is a 1.91% of reference with a coverageData >= 15X There is a 1.84% of reference with a coverageData >= 16X There is a 1.79% of reference with a coverageData >= 17X There is a 1.74% of reference with a coverageData >= 18X There is a 1.69% of reference with a coverageData >= 19X There is a 1.64% of reference with a coverageData >= 20X There is a 1.6% of reference with a coverageData >= 21X There is a 1.55% of reference with a coverageData >= 22X There is a 1.51% of reference with a coverageData >= 23X There is a 1.48% of reference with a coverageData >= 24X There is a 1.44% of reference with a coverageData >= 25X There is a 1.41% of reference with a coverageData >= 26X There is a 1.37% of reference with a coverageData >= 27X There is a 1.34% of reference with a coverageData >= 28X There is a 1.31% of reference with a coverageData >= 29X There is a 1.28% of reference with a coverageData >= 30X There is a 1.25% of reference with a coverageData >= 31X There is a 1.23% of reference with a coverageData >= 32X There is a 1.2% of reference with a coverageData >= 33X There is a 1.18% of reference with a coverageData >= 34X There is a 1.15% of reference with a coverageData >= 35X There is a 1.13% of reference with a coverageData >= 36X There is a 1.11% of reference with a coverageData >= 37X There is a 1.09% of reference with a coverageData >= 38X There is a 1.06% of reference with a coverageData >= 39X There is a 1.04% of reference with a coverageData >= 40X There is a 1.02% of reference with a coverageData >= 41X There is a 1.01% of reference with a coverageData >= 42X There is a 0.99% of reference with a coverageData >= 43X There is a 0.97% of reference with a coverageData >= 44X There is a 0.95% of reference with a coverageData >= 45X There is a 0.93% of reference with a coverageData >= 46X There is a 0.92% of reference with a coverageData >= 47X There is a 0.9% of reference with a coverageData >= 48X There is a 0.89% of reference with a coverageData >= 49X There is a 0.87% of reference with a coverageData >= 50X There is a 0.86% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 553067059 2.218919482651961 20.198050861345095 chr2 243199373 400608654 1.6472437780503653 15.324929406758809 chr3 198022430 292004646 1.474603892094446 14.347550039723712 chr4 191154276 225864332 1.1815813735707381 13.103894200950515 chr5 180915260 355400413 1.9644579069781067 20.00063451078817 chr6 171115067 195015020 1.1396718209507524 12.018032613274759 chr7 159138663 267648933 1.681859882158241 18.31387930387902 chr8 146364022 301405869 2.0592893313631406 39.46092883124082 chr9 141213431 135095549 0.9566763447593026 10.36550197213994 chr10 135534747 269973591 1.991914228459806 18.314186053553808 chr11 135006516 259816012 1.9244701640919317 16.695807358004018 chr12 133851895 276650317 2.066839001420189 17.506151217694747 chr13 115169878 73825107 0.6410105513874036 9.111717443709923 chr14 107349540 159346702 1.4843724714609863 14.26450133445962 chr15 102531392 266823032 2.6023545257241802 23.07855988186527 chr16 90354753 252888654 2.798841738851303 26.389186554649466 chr17 81195210 221723285 2.730743414543789 19.321892727507976 chr18 78077248 62229191 0.7970208043193325 9.260111958249372 chr19 59128983 260921220 4.412746622075336 30.69740139801447 chr20 63025520 137346552 2.1792212424427437 20.2749460228823 chr21 48129895 58039138 1.2058854065648803 13.702411818696238 chr22 51304566 74412860 1.4504139845954451 13.68437482124149 chrMT 16571 13885 0.8379096011103735 3.4787788707059897 chrX 155270560 394794074 2.5426202752150826 27.052769574907284 chrY 59373566 3216181 0.05416856720379571 2.1134723758308342