BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524666.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 = 1,519,209 number of mapped reads = 1,408,561 (92.72%) number of supplementary alignments = 6,505 (0.43%) number of secondary alignments = 0 number of mapped bases = 83,380,073 bp number of sequenced bases = 83,355,242 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,810 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8117 >>>>>>> ACTG content number of A's = 20,914,990 bp (25.09%) number of C's = 15,740,795 bp (18.88%) number of T's = 26,526,851 bp (31.82%) number of G's = 20,161,072 bp (24.19%) number of N's = 11,534 bp (0.01%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 416,449 number of insertions = 5,964 mapped reads with insertion percentage = 0.42% number of deletions = 15,607 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.41% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.258X There is a 2.43% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6872058 0.027570876142370776 0.4370843110726228 chr2 243199373 7059853 0.029029075662954113 0.33990001255899627 chr3 198022430 5514323 0.027846961579049402 0.18083337555411386 chr4 191154276 5403726 0.02826892556669776 0.20325562647176537 chr5 180915260 4997426 0.027623020855178274 0.18154884954759393 chr6 171115067 4726965 0.027624481484146573 0.2005477802642565 chr7 159138663 4538349 0.028518204906622848 0.3036453682140802 chr8 146364022 4261040 0.02911261894675182 0.26900797330575377 chr9 141213431 3514441 0.024887441478565874 0.2183056216625916 chr10 135534747 4032787 0.029754635540065605 0.2670884652282551 chr11 135006516 3808136 0.02820705335437291 0.22767561295568506 chr12 133851895 3735422 0.027907128247978856 0.18277691919467104 chr13 115169878 2549654 0.02213820179613284 0.16162451513570233 chr14 107349540 2502747 0.023313998364594763 0.17097103861675308 chr15 102531392 2385806 0.023269029645086647 0.16659279327147677 chr16 90354753 2493214 0.027593612037210703 0.1913559378780736 chr17 81195210 2195546 0.027040338955955652 0.19199255041164243 chr18 78077248 2268375 0.029052957911631313 0.41632958779520784 chr19 59128983 1723918 0.02915521141298845 0.3647900571692661 chr20 63025520 1795741 0.02849228376060999 0.18558897498350999 chr21 48129895 1098943 0.0228328567930597 0.18679289229792176 chr22 51304566 1017576 0.019834024129548235 0.153478428056762 chrMT 16571 20497 1.2369199203427674 1.340154463262362 chrX 155270560 4585149 0.029530060302481037 0.20287993374942273 chrY 59373566 278381 0.004688635343209805 0.1696648091573225