BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716471.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 = 524,490 number of mapped reads = 477,458 (91.03%) number of supplementary alignments = 1,502 (0.29%) number of secondary alignments = 0 number of mapped bases = 27,923,213 bp number of sequenced bases = 27,914,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,155 duplication rate = 1.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6006 >>>>>>> ACTG content number of A's = 7,005,525 bp (25.1%) number of C's = 5,220,259 bp (18.7%) number of T's = 8,504,981 bp (30.47%) number of G's = 7,183,595 bp (25.73%) number of N's = 548 bp (0%) GC percentage = 44.43% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 151,957 number of insertions = 1,739 mapped reads with insertion percentage = 0.36% number of deletions = 5,215 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.009X std coverageData = 0.1177X There is a 0.86% of reference with a coverageData >= 1X There is a 0.03% 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 2331141 0.009352598563836677 0.16620225920741927 chr2 243199373 2221495 0.009134460227411852 0.14250673351374213 chr3 198022430 1631534 0.008239137354288602 0.09301795473524158 chr4 191154276 1778350 0.009303218516545243 0.1040004551987963 chr5 180915260 1601509 0.00885226044502824 0.09640482523066704 chr6 171115067 1516149 0.00886040619672609 0.10296837777732427 chr7 159138663 1596177 0.010030101861544483 0.14625226222137638 chr8 146364022 1481374 0.010121162152813756 0.1368443467988878 chr9 141213431 917352 0.00649620927346493 0.09015574682923323 chr10 135534747 1231739 0.009087994239587874 0.12430765741202532 chr11 135006516 995887 0.007376584697586004 0.10037159416357429 chr12 133851895 1378135 0.010295969287547255 0.10458500772486727 chr13 115169878 855694 0.007429842028659612 0.08843726827370979 chr14 107349540 935320 0.00871284590506862 0.09659288393606097 chr15 102531392 1018990 0.009938322109193641 0.10295922662100218 chr16 90354753 922295 0.010207487369258814 0.10718172029968884 chr17 81195210 1181903 0.014556314344158971 0.12614830540960154 chr18 78077248 519537 0.0066541407811914685 0.12862005005655297 chr19 59128983 681323 0.011522657171357066 0.14630278880509168 chr20 63025520 896185 0.014219398745143236 0.1238696819531249 chr21 48129895 355779 0.007392058511658918 0.09524289000593131 chr22 51304566 247419 0.004822553220701643 0.07116798143444737 chrMT 16571 1546 0.09329551626335164 0.2972085782428956 chrX 155270560 1529634 0.009851410338186454 0.10481419666481703 chrY 59373566 96746 0.0016294456694752005 0.07602368808883349