BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525014.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 = 1,066,093 number of mapped reads = 956,636 (89.73%) number of supplementary alignments = 4,139 (0.39%) number of secondary alignments = 0 number of mapped bases = 55,068,971 bp number of sequenced bases = 55,051,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,739 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2233 >>>>>>> ACTG content number of A's = 13,945,111 bp (25.33%) number of C's = 10,206,014 bp (18.54%) number of T's = 17,627,965 bp (32.02%) number of G's = 13,271,624 bp (24.11%) number of N's = 603 bp (0%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 277,872 number of insertions = 3,264 mapped reads with insertion percentage = 0.34% number of deletions = 10,464 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.11% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.1815X There is a 1.66% of reference with a coverageData >= 1X There is a 0.08% 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 5904315 0.023688265956216013 0.31435629383427954 chr2 243199373 5085257 0.020909827756833897 0.20432049465534874 chr3 198022430 3073389 0.015520408470898979 0.13065984325830782 chr4 191154276 3571358 0.018683118550798204 0.15044020288322626 chr5 180915260 2407190 0.013305621648499966 0.12198500267500531 chr6 171115067 3245039 0.018964075209110604 0.18608072292547548 chr7 159138663 3481803 0.021879051478520966 0.22824097337866345 chr8 146364022 3759248 0.025684235433213225 0.19551867227434602 chr9 141213431 1467682 0.01039335982141812 0.13756430213060353 chr10 135534747 2807284 0.020712651642017674 0.18448107345359735 chr11 135006516 2367825 0.01753859791478509 0.1689925008236402 chr12 133851895 3008957 0.022479748979272948 0.15808585353982757 chr13 115169878 1076215 0.00934458747972278 0.1023702716983667 chr14 107349540 1253206 0.011674069586138888 0.11605601522788479 chr15 102531392 1548141 0.015099190304565455 0.138039691189237 chr16 90354753 1788623 0.019795560727170602 0.1517793788464743 chr17 81195210 1630427 0.020080334788222114 0.19619730072566646 chr18 78077248 1100267 0.014092031010109373 0.20521636227542395 chr19 59128983 1373951 0.023236506536904244 0.2203988011597534 chr20 63025520 1042784 0.01654542477396458 0.13533770075596221 chr21 48129895 800664 0.016635481959808972 0.1399262794401529 chr22 51304566 762669 0.014865518987140443 0.12701429327789956 chrMT 16571 9372 0.5655663508539014 0.8696942094408735 chrX 155270560 2353721 0.015158836291953864 0.14491036021118806 chrY 59373566 149584 0.0025193703204554026 0.06961227591577966