BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717091.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 = 713,522 number of mapped reads = 657,400 (92.13%) number of supplementary alignments = 10,094 (1.41%) number of secondary alignments = 0 number of mapped bases = 51,874,833 bp number of sequenced bases = 51,852,580 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,858 duplication rate = 1.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9111 >>>>>>> ACTG content number of A's = 12,892,840 bp (24.86%) number of C's = 10,106,170 bp (19.49%) number of T's = 16,088,407 bp (31.03%) number of G's = 12,762,414 bp (24.61%) number of N's = 2,749 bp (0.01%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 428,930 number of insertions = 4,520 mapped reads with insertion percentage = 0.68% number of deletions = 12,961 mapped reads with deletion percentage = 1.94% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 0.2245X There is a 1.54% of reference with a coverageData >= 1X There is a 0.08% 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 4105398 0.016470963978059656 0.3461065180648518 chr2 243199373 4454429 0.018315955937929167 0.31875720438955707 chr3 198022430 3435108 0.017347065178424485 0.13903326270760694 chr4 191154276 3361859 0.01758715039155075 0.14710769339463134 chr5 180915260 3099227 0.01713082135802143 0.13940657959201877 chr6 171115067 2952038 0.017251771289082334 0.16101283791389848 chr7 159138663 2877555 0.018082060925697235 0.2875682388247162 chr8 146364022 2704432 0.018477437030255974 0.2957770477550941 chr9 141213431 2237431 0.015844321493753664 0.24300993584905403 chr10 135534747 2425016 0.017892208851800935 0.2065312249704905 chr11 135006516 2334203 0.017289558083255774 0.21788732401651498 chr12 133851895 2339300 0.01747677909229451 0.14184509259831019 chr13 115169878 1597415 0.01387007634062094 0.12351816761123319 chr14 107349540 1567439 0.014601264243889633 0.1596492799148269 chr15 102531392 1460072 0.01424024361241482 0.1272213978631042 chr16 90354753 1492742 0.016520901783661564 0.14853023891275438 chr17 81195210 1420139 0.017490428314675212 0.15020089998130945 chr18 78077248 1470375 0.018832310790462287 0.4221976222902698 chr19 59128983 1101216 0.018623963141730343 0.2635294519790187 chr20 63025520 1034715 0.016417397270185156 0.1399795082550792 chr21 48129895 696171 0.014464419670975804 0.13250268745002977 chr22 51304566 575119 0.011209898939599255 0.11126338805666446 chrMT 16571 6411 0.38688069519039286 0.7030502378236507 chrX 155270560 2983957 0.019217789901704484 0.18326596901235284 chrY 59373566 143066 0.0024095908270020364 0.07433906931034456