BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008670.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 = 1,562,713 number of mapped reads = 1,406,689 (90.02%) number of supplementary alignments = 8,418 (0.54%) number of secondary alignments = 0 number of mapped bases = 94,346,400 bp number of sequenced bases = 94,296,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,120 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6691 >>>>>>> ACTG content number of A's = 27,307,820 bp (28.96%) number of C's = 17,376,639 bp (18.43%) number of T's = 29,444,363 bp (31.23%) number of G's = 20,150,277 bp (21.37%) number of N's = 16,905 bp (0.02%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 694,181 number of insertions = 8,097 mapped reads with insertion percentage = 0.57% number of deletions = 30,301 mapped reads with deletion percentage = 2.13% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.2867X There is a 2.72% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9624330 0.038613063274975754 0.4352038081178497 chr2 243199373 8950960 0.03680502909849196 0.30341552788238074 chr3 198022430 7172862 0.036222472373457895 0.2158400160737704 chr4 191154276 5948463 0.031118649943253165 0.20030149914385945 chr5 180915260 1580723 0.008737366875519511 0.10576260745379905 chr6 171115067 9047923 0.05287624964083379 0.30457180872195816 chr7 159138663 5557750 0.03492394554050011 0.35367174403163554 chr8 146364022 4025450 0.02750300206972995 0.44480738067836023 chr9 141213431 5766763 0.040837213281787625 0.29474692380952455 chr10 135534747 6822286 0.050336066219240444 0.48734410012386487 chr11 135006516 3671155 0.027192428252870403 0.22001881052110717 chr12 133851895 7253566 0.05419098474474343 0.25426913189374106 chr13 115169878 2263840 0.019656528593353203 0.14994154570925933 chr14 107349540 1095053 0.01020081688286694 0.12603812924238894 chr15 102531392 1735306 0.016924631238791725 0.1414778753018015 chr16 90354753 1978936 0.02190184726640778 0.1882748354332216 chr17 81195210 3371541 0.04152389038712998 0.22952562666052256 chr18 78077248 1402387 0.017961532148264243 0.40492088231593854 chr19 59128983 1275456 0.021570741373989132 0.3019666963748008 chr20 63025520 2127294 0.03375289882574551 0.20109043879719282 chr21 48129895 1251739 0.026007515703078098 0.18690702960857938 chr22 51304566 1110971 0.021654427405155323 0.15747356780390806 chrMT 16571 69185 4.175064872367389 3.1425772117734514 chrX 155270560 1044521 0.006727102678060799 0.11562136768932212 chrY 59373566 197940 0.0033338068324883837 0.12362090876665537