BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818822.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,092,769 number of mapped reads = 2,032,278 (97.11%) number of supplementary alignments = 16,836 (0.8%) number of secondary alignments = 0 number of mapped bases = 138,140,039 bp number of sequenced bases = 138,079,818 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 992,372 duplication rate = 39.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8015 >>>>>>> ACTG content number of A's = 40,090,565 bp (29.03%) number of C's = 27,270,092 bp (19.75%) number of T's = 39,891,871 bp (28.89%) number of G's = 30,818,625 bp (22.32%) number of N's = 8,665 bp (0.01%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 739,751 number of insertions = 19,365 mapped reads with insertion percentage = 0.94% number of deletions = 36,695 mapped reads with deletion percentage = 1.79% homopolymer indels = 40.67% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.5847X There is a 1.94% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% 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 11453030 0.04594985542683964 0.7992922337685082 chr2 243199373 12375534 0.0508863729677461 0.9756891650557288 chr3 198022430 9343511 0.04718410434615917 0.43469045349497604 chr4 191154276 8886667 0.0464895014956401 0.47613245904095153 chr5 180915260 8565639 0.04734613873920862 0.44797753985850486 chr6 171115067 8241689 0.048164601425776256 0.47599504455415975 chr7 159138663 7543471 0.04740187492966433 0.4981329922595029 chr8 146364022 6984500 0.04772006060341796 0.4723720720628191 chr9 141213431 5977174 0.042327234439902536 0.4714214362268465 chr10 135534747 6830828 0.05039909064795023 0.6660253515644936 chr11 135006516 6484472 0.048030807638943886 0.48691260651283313 chr12 133851895 6332711 0.047311328689070856 0.45576430537915963 chr13 115169878 4428792 0.038454429898762243 0.38396757114252017 chr14 107349540 4336160 0.04039290713309065 0.46251187816599587 chr15 102531392 4027258 0.039278292447253615 0.3952273673401726 chr16 90354753 4016240 0.04444968157900891 0.689236524476661 chr17 81195210 3623435 0.04462621625093401 0.4438072267490845 chr18 78077248 3647300 0.0467139927882704 0.6141132294322655 chr19 59128983 2696383 0.04560171447562357 0.6741168290801633 chr20 63025520 3049369 0.04838308355091715 0.48175340398443023 chr21 48129895 1841325 0.03825740737643413 0.41625252603985646 chr22 51304566 1651176 0.03218380212006861 0.3951847134023513 chrMT 16571 195651 11.806831211152012 11.73119078853031 chrX 155270560 4284074 0.027591025626493522 0.3548862593907486 chrY 59373566 1323650 0.02229359105700338 1.020926030586207