BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524577.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,333,597 number of mapped reads = 2,144,463 (91.9%) number of supplementary alignments = 8,076 (0.35%) number of secondary alignments = 0 number of mapped bases = 124,905,098 bp number of sequenced bases = 124,872,367 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,115 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6428 >>>>>>> ACTG content number of A's = 31,821,334 bp (25.48%) number of C's = 23,747,126 bp (19.02%) number of T's = 39,473,567 bp (31.61%) number of G's = 29,826,447 bp (23.89%) number of N's = 3,893 bp (0%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 598,678 number of insertions = 6,823 mapped reads with insertion percentage = 0.32% number of deletions = 19,586 mapped reads with deletion percentage = 0.91% homopolymer indels = 43.08% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.3401X There is a 3.51% of reference with a coverageData >= 1X There is a 0.37% 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 0.01% 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 9132884 0.03664136909010951 0.5613414212268061 chr2 243199373 8678853 0.03568616519418411 0.3669824872164297 chr3 198022430 7694508 0.03885674971264619 0.21721299925941953 chr4 191154276 7892095 0.04128652084141712 0.26174877146269027 chr5 180915260 7000421 0.03869447497132083 0.21959357012142897 chr6 171115067 6512975 0.038061960961041495 0.2390267868901024 chr7 159138663 8065092 0.05067965161929254 0.4692346042936949 chr8 146364022 5449696 0.03723384972298725 0.3579497601991399 chr9 141213431 5984051 0.042375933773608265 0.3473026766583872 chr10 135534747 4741022 0.03498012210846566 0.36203623320250394 chr11 135006516 4912340 0.03638594747530556 0.28443198623755606 chr12 133851895 9427473 0.07043212201067456 0.3417065290771564 chr13 115169878 4616274 0.04008230346480006 0.22024148517489464 chr14 107349540 4504991 0.04196562928914274 0.2430362576466734 chr15 102531392 3240266 0.03160267247712779 0.19696745022321674 chr16 90354753 3546506 0.039250906922406174 0.23924327191776534 chr17 81195210 3816541 0.04700450925614947 0.25049082800864314 chr18 78077248 4011959 0.05138448271127589 0.6394469870101643 chr19 59128983 2113286 0.03574027309077851 0.41833482308365605 chr20 63025520 3737384 0.0592995345377555 0.27954137932525225 chr21 48129895 1492632 0.031012575448169998 0.23055897892562957 chr22 51304566 1236995 0.02411081695925466 0.16983441877821595 chrMT 16571 18964 1.1444089071269083 1.3406845391116715 chrX 155270560 6721898 0.04329151643428091 0.27431792665492843 chrY 59373566 355992 0.005995799544868166 0.1514710952362475