BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716630.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 = 596,201 number of mapped reads = 533,036 (89.41%) number of supplementary alignments = 2,687 (0.45%) number of secondary alignments = 0 number of mapped bases = 31,593,763 bp number of sequenced bases = 31,583,771 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,576 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6021 >>>>>>> ACTG content number of A's = 8,271,174 bp (26.19%) number of C's = 6,100,091 bp (19.31%) number of T's = 9,401,533 bp (29.77%) number of G's = 7,810,085 bp (24.73%) number of N's = 888 bp (0%) GC percentage = 44.04% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 156,073 number of insertions = 2,434 mapped reads with insertion percentage = 0.45% number of deletions = 6,021 mapped reads with deletion percentage = 1.12% homopolymer indels = 40.76% >>>>>>> Coverage mean coverageData = 0.0102X std coverageData = 0.119X There is a 0.97% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2597435 0.010420977045429308 0.1667443873432809 chr2 243199373 2573305 0.01058105112795665 0.1302673359441441 chr3 198022430 2109444 0.01065255082467173 0.10697062925303981 chr4 191154276 2063137 0.010793046554710604 0.11148266343347717 chr5 180915260 1937290 0.01070827303346329 0.10745097694782271 chr6 171115067 1797529 0.010504796751767043 0.11370756132862295 chr7 159138663 1711420 0.010754269061566768 0.12935961335064616 chr8 146364022 1547907 0.010575734247040574 0.12040727144698296 chr9 141213431 1337859 0.009474020923689618 0.10876594939317585 chr10 135534747 1477058 0.010898002414096808 0.12356458496986515 chr11 135006516 1423344 0.010542780024039728 0.11510255118132721 chr12 133851895 1447287 0.010812600000918927 0.10792980679863509 chr13 115169878 1013880 0.00880334352702883 0.09734900841216522 chr14 107349540 915773 0.008530758492304672 0.0980621692926474 chr15 102531392 932356 0.009093371130667962 0.09929041047911168 chr16 90354753 925807 0.010246356381495503 0.10774464702011853 chr17 81195210 884360 0.010891775512373206 0.11018195610274609 chr18 78077248 832356 0.010660672876175144 0.15374854013151235 chr19 59128983 653508 0.011052244886403677 0.1335751712918477 chr20 63025520 688686 0.010927097467819384 0.10891074029545415 chr21 48129895 422226 0.008772634970427424 0.10192722677492706 chr22 51304566 395084 0.007700757082712677 0.09125243712884912 chrMT 16571 4757 0.2870677689940257 0.5824365294501495 chrX 155270560 1805283 0.011626692143056611 0.11452523795485557 chrY 59373566 96672 0.0016281993235845056 0.055307017125030174