BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238049.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,150,139 number of mapped reads = 614,605 (53.44%) number of supplementary alignments = 6,141 (0.53%) number of secondary alignments = 0 number of mapped bases = 36,983,144 bp number of sequenced bases = 36,964,448 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,253 duplication rate = 8.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7347 >>>>>>> ACTG content number of A's = 9,647,167 bp (26.1%) number of C's = 6,395,462 bp (17.3%) number of T's = 12,012,352 bp (32.5%) number of G's = 8,907,950 bp (24.1%) number of N's = 1,517 bp (0%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 300,876 number of insertions = 2,807 mapped reads with insertion percentage = 0.45% number of deletions = 11,756 mapped reads with deletion percentage = 1.89% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.0119X std coverageData = 0.1632X There is a 0.89% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 2842167 0.011402848219984977 0.2298413496077405 chr2 243199373 3232569 0.01329184759041299 0.20645776930557433 chr3 198022430 2888432 0.014586388016751436 0.15718790641429697 chr4 191154276 2193144 0.011473162127955745 0.14035237539909173 chr5 180915260 2169721 0.011993023695181931 0.14161968091725413 chr6 171115067 2249657 0.013147042159648046 0.16231726159039958 chr7 159138663 1914258 0.012028868182711828 0.16232750670166432 chr8 146364022 2057350 0.014056391535892611 0.17563675328328876 chr9 141213431 1477155 0.010460442675597904 0.1413387483212688 chr10 135534747 1706414 0.012590232672954338 0.15871950416647143 chr11 135006516 1615827 0.01196851120874788 0.14711367142804166 chr12 133851895 1745308 0.013039098176383681 0.1474563451470188 chr13 115169878 1366173 0.011862242313046473 0.14366901477025226 chr14 107349540 1044218 0.009727270373026285 0.13246630838053203 chr15 102531392 936754 0.00913626531082305 0.12307614566803834 chr16 90354753 958908 0.010612701248820857 0.1348313091040291 chr17 81195210 992944 0.012229095780403794 0.1451505325205304 chr18 78077248 1088951 0.013947097623112945 0.22095555790465457 chr19 59128983 680312 0.01150555895744055 0.1667427327265615 chr20 63025520 870206 0.013807200638725392 0.15346634856205607 chr21 48129895 564398 0.011726557890890891 0.1429707962754325 chr22 51304566 389083 0.007583788936056881 0.10974150721688615 chrMT 16571 21048 1.2701707802788003 2.0173887548971257 chrX 155270560 1875831 0.012081047431013323 0.14611073755645254 chrY 59373566 102316 0.0017232584615180433 0.05333226895094149