BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525029.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 = 871,415 number of mapped reads = 776,602 (89.12%) number of supplementary alignments = 2,756 (0.32%) number of secondary alignments = 0 number of mapped bases = 44,812,655 bp number of sequenced bases = 44,797,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,322 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.281 >>>>>>> ACTG content number of A's = 11,377,445 bp (25.4%) number of C's = 8,300,969 bp (18.53%) number of T's = 14,442,534 bp (32.24%) number of G's = 10,676,206 bp (23.83%) number of N's = 400 bp (0%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 228,855 number of insertions = 2,942 mapped reads with insertion percentage = 0.38% number of deletions = 8,927 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.3% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1562X There is a 1.36% of reference with a coverageData >= 1X There is a 0.06% 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 3577780 0.014354146784653347 0.24020233432571964 chr2 243199373 3791857 0.015591557466720935 0.18432238852811939 chr3 198022430 2950514 0.014899897956004276 0.127799605877461 chr4 191154276 2873891 0.015034406031283339 0.13874639504221362 chr5 180915260 2691586 0.014877606233990433 0.12807861092807563 chr6 171115067 2606700 0.01523360885572981 0.14625907280215628 chr7 159138663 2443648 0.015355463932733933 0.17871415072517138 chr8 146364022 2257407 0.015423237002874927 0.16166893036206134 chr9 141213431 1861861 0.013184730282489914 0.13726400720454907 chr10 135534747 2258813 0.016665932906489284 0.16878570616164368 chr11 135006516 2051259 0.015193777758104654 0.1541501251940219 chr12 133851895 2019976 0.015091127398681953 0.1298068595486935 chr13 115169878 1393383 0.012098502005880392 0.11550097197883633 chr14 107349540 1372748 0.01278764678451347 0.12076082178555463 chr15 102531392 1273879 0.012424282701633467 0.11773651983629209 chr16 90354753 1310110 0.014499624607462543 0.13052803916152594 chr17 81195210 1218048 0.015001476072295399 0.13634367334449926 chr18 78077248 1201211 0.015384904447451836 0.1978453905733761 chr19 59128983 916553 0.015500909257986055 0.18009103331302542 chr20 63025520 969945 0.015389718323625097 0.13134199688268944 chr21 48129895 595226 0.012367074559377285 0.12290467833119521 chr22 51304566 559260 0.01090078415242807 0.1093078155310065 chrMT 16571 2420 0.14603825961016234 0.39370670968509736 chrX 155270560 2473809 0.01593224755549281 0.13945499062205133 chrY 59373566 140771 0.0023709372618784595 0.08213338553942866