BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716233.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 = 3,677,627 number of mapped reads = 3,234,431 (87.95%) number of supplementary alignments = 11,499 (0.31%) number of secondary alignments = 0 number of mapped bases = 183,192,908 bp number of sequenced bases = 183,140,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,844 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0619 >>>>>>> ACTG content number of A's = 44,812,607 bp (24.47%) number of C's = 36,088,943 bp (19.71%) number of T's = 57,119,791 bp (31.19%) number of G's = 45,118,236 bp (24.64%) number of N's = 1,420 bp (0%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 961,864 number of insertions = 12,059 mapped reads with insertion percentage = 0.37% number of deletions = 32,694 mapped reads with deletion percentage = 1% homopolymer indels = 41.04% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.4197X There is a 4.97% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16117545 0.06466401140882212 0.5333371723342542 chr2 243199373 14531419 0.059751054539108533 0.6586935452881421 chr3 198022430 10507377 0.0530615496436439 0.27955493150791194 chr4 191154276 11525788 0.060295737250470924 0.3153987815125338 chr5 180915260 10612311 0.05865901527599164 0.27954414122243104 chr6 171115067 9790651 0.05721676747495298 0.36110449082529367 chr7 159138663 10572079 0.06643312693911473 0.6694977675506424 chr8 146364022 9350065 0.06388226336114212 0.3830149849526933 chr9 141213431 6030331 0.042703664639378386 0.3023433929915114 chr10 135534747 8020731 0.05917841127485928 0.5413044297100748 chr11 135006516 6452875 0.047796767083449515 0.3584916880344444 chr12 133851895 9237165 0.06901034161675484 0.31119913208623523 chr13 115169878 5466151 0.04746163749517908 0.2536732697960724 chr14 107349540 6104458 0.05686524599919105 0.30095094682040824 chr15 102531392 6713558 0.06547807329095853 0.31206645862460664 chr16 90354753 6393306 0.0707578272058361 0.34003019366597903 chr17 81195210 8116964 0.09996850799449869 0.40404561060009736 chr18 78077248 3379153 0.04327961200681663 0.5065927657260143 chr19 59128983 4693093 0.07937043327804234 0.5343982666314163 chr20 63025520 5247415 0.08325857525649927 0.36178629124252437 chr21 48129895 2236363 0.046465154349495254 0.27554938208034285 chr22 51304566 1697553 0.033087756750539515 0.21260253092640455 chrMT 16571 24952 1.5057630800796573 1.6252307074205832 chrX 155270560 9856817 0.06348155761143645 0.32994916027589527 chrY 59373566 514788 0.008670323086203042 0.21086432705554137