BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716751.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 = 1,165,649 number of mapped reads = 1,064,485 (91.32%) number of supplementary alignments = 4,078 (0.35%) number of secondary alignments = 0 number of mapped bases = 60,955,842 bp number of sequenced bases = 60,939,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,505 duplication rate = 1.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3391 >>>>>>> ACTG content number of A's = 15,367,309 bp (25.22%) number of C's = 12,873,739 bp (21.13%) number of T's = 18,040,697 bp (29.6%) number of G's = 14,656,692 bp (24.05%) number of N's = 1,293 bp (0%) GC percentage = 45.18% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 297,098 number of insertions = 3,157 mapped reads with insertion percentage = 0.3% number of deletions = 9,405 mapped reads with deletion percentage = 0.88% homopolymer indels = 43.8% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.1783X There is a 1.82% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4963421 0.01991337465915481 0.24359690684607152 chr2 243199373 5144376 0.021152916376967798 0.19686834800648986 chr3 198022430 4105997 0.020735009665319225 0.15289978009496213 chr4 191154276 3787867 0.019815758659774894 0.15821977288037659 chr5 180915260 3689007 0.020390800643350925 0.1525772348038041 chr6 171115067 3490955 0.02040121341272654 0.1588169127452017 chr7 159138663 3338751 0.020980137303277458 0.20017997134577967 chr8 146364022 3091429 0.02112150894568885 0.1714188878448561 chr9 141213431 2565003 0.018164015857670083 0.18413012251877842 chr10 135534747 2925872 0.021587615462181076 0.18277406241518854 chr11 135006516 2781212 0.02060057604923306 0.18034203993124057 chr12 133851895 2738098 0.02045617658233378 0.15366303342724266 chr13 115169878 1873856 0.01627036541620718 0.1349212509985903 chr14 107349540 1872204 0.017440261038845627 0.14998496016781843 chr15 102531392 1755498 0.01712156604681618 0.1390980116003348 chr16 90354753 1801851 0.01994196143726938 0.15853736830729434 chr17 81195210 1689672 0.020809996057649213 0.15968520390279103 chr18 78077248 1638607 0.020986997390071944 0.29927079917430405 chr19 59128983 1308210 0.02212468291565238 0.2031825409399585 chr20 63025520 1360582 0.021587794912283152 0.15892620030065285 chr21 48129895 787439 0.016360704713775088 0.1489711549919997 chr22 51304566 755837 0.01473235345173761 0.12928252763185064 chrMT 16571 2557 0.15430571480296904 0.39977969668391566 chrX 155270560 3318946 0.021375243317213515 0.17111673018136672 chrY 59373566 168595 0.0028395633167797264 0.07167765099463609