BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716359.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 = 6,332,532 number of mapped reads = 5,826,937 (92.02%) number of supplementary alignments = 32,327 (0.51%) number of secondary alignments = 0 number of mapped bases = 339,030,756 bp number of sequenced bases = 338,937,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 483,348 duplication rate = 6.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7038 >>>>>>> ACTG content number of A's = 90,610,282 bp (26.73%) number of C's = 68,552,870 bp (20.23%) number of T's = 103,162,722 bp (30.44%) number of G's = 76,605,970 bp (22.6%) number of N's = 5,269 bp (0%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,745,371 number of insertions = 24,634 mapped reads with insertion percentage = 0.42% number of deletions = 56,059 mapped reads with deletion percentage = 0.96% homopolymer indels = 42.07% >>>>>>> Coverage mean coverageData = 0.1095X std coverageData = 0.8535X There is a 8.23% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 24631241 0.09882118207440695 1.6269967204468099 chr2 243199373 28721434 0.1180983061169323 0.9863855747944392 chr3 198022430 20802377 0.10505060967083375 0.4049326843634653 chr4 191154276 21266616 0.11125367658529386 0.543241788326111 chr5 180915260 17800027 0.09838875393927522 0.40997460025848753 chr6 171115067 15270002 0.08923820834549888 0.48352761257285615 chr7 159138663 21331155 0.1340413108786769 1.174501647050125 chr8 146364022 14734593 0.10067086705228694 0.8420402805741658 chr9 141213431 16056606 0.1137045243238938 0.9207540220122692 chr10 135534747 12737026 0.09397609308261003 0.8029209154853948 chr11 135006516 13089198 0.0969523426558167 0.7105392556384664 chr12 133851895 25258070 0.18870162428406412 0.7134106896087146 chr13 115169878 13034183 0.11317354178320828 0.4224971740337762 chr14 107349540 12378813 0.1153131443320577 0.513792600743645 chr15 102531392 8852393 0.08633836747286139 0.369447612986254 chr16 90354753 9671839 0.10704294659518354 0.49510767573962094 chr17 81195210 9533195 0.1174108053911062 0.4741316850723763 chr18 78077248 10897437 0.1395725038874321 1.7546704514892062 chr19 59128983 5783766 0.09781609130669472 1.1989058291949921 chr20 63025520 10927569 0.1733832422168036 0.5675053932138664 chr21 48129895 4232918 0.08794779211548248 0.4862426037656334 chr22 51304566 3450441 0.06725407247378333 0.31858576459619403 chrMT 16571 83300 5.026854142779555 3.91338873885878 chrX 155270560 17567734 0.11314272325674617 0.6127391965682117 chrY 59373566 918823 0.01547528743683679 0.32314188434303653