BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716517.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 = 952,131 number of mapped reads = 754,260 (79.22%) number of supplementary alignments = 2,861 (0.3%) number of secondary alignments = 0 number of mapped bases = 41,428,407 bp number of sequenced bases = 41,416,503 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,414 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.2923 >>>>>>> ACTG content number of A's = 9,592,221 bp (23.16%) number of C's = 8,859,480 bp (21.39%) number of T's = 12,776,883 bp (30.85%) number of G's = 10,186,788 bp (24.6%) number of N's = 1,131 bp (0%) GC percentage = 45.99% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 228,548 number of insertions = 3,141 mapped reads with insertion percentage = 0.41% number of deletions = 7,089 mapped reads with deletion percentage = 0.93% homopolymer indels = 34.96% >>>>>>> Coverage mean coverageData = 0.0134X std coverageData = 0.1397X There is a 1.24% of reference with a coverageData >= 1X There is a 0.07% 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 3947716 0.015838339676594024 0.160098197290204 chr2 243199373 3533469 0.014529104069688535 0.17484088240001985 chr3 198022430 2767491 0.013975644072239696 0.12871052004607886 chr4 191154276 2673940 0.013988387055490195 0.13935694463772844 chr5 180915260 2536450 0.014020099796998883 0.12751275951663402 chr6 171115067 1804749 0.010546990581489822 0.11165979605869802 chr7 159138663 2449829 0.015394304274128532 0.156927519828986 chr8 146364022 2506156 0.017122759854194224 0.1469986233058201 chr9 141213431 1767864 0.012519092465078622 0.12760299678672915 chr10 135534747 2162036 0.01595189460898909 0.1907184171101196 chr11 135006516 1731967 0.01282876598341372 0.1398493329944723 chr12 133851895 2016456 0.015064829676113289 0.13218494462751998 chr13 115169878 752285 0.006531959684805778 0.08683799786280334 chr14 107349540 1294471 0.012058468066095113 0.11935242885422565 chr15 102531392 824166 0.008038182101341216 0.09634466694517363 chr16 90354753 1123927 0.012439046787057234 0.1278792136252661 chr17 81195210 1662119 0.02047065337967597 0.1589477899981765 chr18 78077248 1109180 0.014206187185286039 0.15034951567748928 chr19 59128983 1172660 0.019832236925164094 0.17076972217402347 chr20 63025520 1071993 0.01700887196170694 0.14556424090757614 chr21 48129895 560746 0.011650679894481382 0.12799463510169412 chr22 51304566 474730 0.009253172514898576 0.10413597445708958 chrMT 16571 22761 1.3735441433830184 1.6004334943505925 chrX 155270560 1324611 0.008530986170205092 0.10606395634556003 chrY 59373566 136635 0.002301276632095839 0.07780542972419789