BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716268.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 = 1,902,212 number of mapped reads = 1,292,437 (67.94%) number of supplementary alignments = 1,510 (0.08%) number of secondary alignments = 0 number of mapped bases = 65,848,834 bp number of sequenced bases = 65,831,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,773 duplication rate = 7.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.352 >>>>>>> ACTG content number of A's = 14,305,297 bp (21.73%) number of C's = 10,370,914 bp (15.75%) number of T's = 22,065,676 bp (33.52%) number of G's = 19,088,437 bp (29%) number of N's = 1,053 bp (0%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 519,651 number of insertions = 4,045 mapped reads with insertion percentage = 0.31% number of deletions = 10,454 mapped reads with deletion percentage = 0.8% homopolymer indels = 41.38% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.2142X There is a 1.81% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 6576093 0.02638345683399521 0.2636599744385445 chr2 243199373 5720710 0.023522716894504494 0.3888641797798614 chr3 198022430 4409962 0.02227001254352853 0.175402194476245 chr4 191154276 4150447 0.021712551175156553 0.18402588216092547 chr5 180915260 4026188 0.022254551661368974 0.1727861240524977 chr6 171115067 2849223 0.016650918296984334 0.1972817690149444 chr7 159138663 3770746 0.02369471961694186 0.21056907717198203 chr8 146364022 3974443 0.027154507956880278 0.2010621387544373 chr9 141213431 2908714 0.020597998217322545 0.1829864984194768 chr10 135534747 3363549 0.02481687592628922 0.22930124459466852 chr11 135006516 2764096 0.020473796983250792 0.1876240710022133 chr12 133851895 3141017 0.02346636183223256 0.17919531785895962 chr13 115169878 1172730 0.010182610421797963 0.12309809474115267 chr14 107349540 2089300 0.019462589220223953 0.1648108034418694 chr15 102531392 1313994 0.012815528730947103 0.13350828169107706 chr16 90354753 1765217 0.01953651514049294 0.17730188877330427 chr17 81195210 2604970 0.03208280389939259 0.2163154042625443 chr18 78077248 1674011 0.021440445749317395 0.20043135003549808 chr19 59128983 1797509 0.03039979564674738 0.2596407604481006 chr20 63025520 1748691 0.027745760764845733 0.2083858666469875 chr21 48129895 906507 0.01883459334370042 0.16798128606592874 chr22 51304566 741332 0.01444963007775955 0.14171834721182622 chrMT 16571 34046 2.0545531349948707 2.1885551436450865 chrX 155270560 2130801 0.013723148805543046 0.1439739852144114 chrY 59373566 214538 0.0036133588472688333 0.10179147959710957