BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524625.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 = 636,655 number of mapped reads = 579,056 (90.95%) number of supplementary alignments = 1,928 (0.3%) number of secondary alignments = 0 number of mapped bases = 33,033,739 bp number of sequenced bases = 33,016,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,346 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8643 >>>>>>> ACTG content number of A's = 8,270,687 bp (25.05%) number of C's = 5,728,273 bp (17.35%) number of T's = 10,492,097 bp (31.78%) number of G's = 8,525,013 bp (25.82%) number of N's = 185 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 186,386 number of insertions = 2,000 mapped reads with insertion percentage = 0.34% number of deletions = 10,447 mapped reads with deletion percentage = 1.79% homopolymer indels = 42.24% >>>>>>> Coverage mean coverageData = 0.0107X std coverageData = 0.1315X There is a 0.95% of reference with a coverageData >= 1X There is a 0.09% 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 3311542 0.013285992976523015 0.18981348578096585 chr2 243199373 2945476 0.01211136346145103 0.1524612164692556 chr3 198022430 2201136 0.011115589279456878 0.11663511932941552 chr4 191154276 1540402 0.00805842292536527 0.10790964702478925 chr5 180915260 1997721 0.011042302346413454 0.11644983160491572 chr6 171115067 2109407 0.012327418251251948 0.1255964682275123 chr7 159138663 2093639 0.013156067548462437 0.15345211356557614 chr8 146364022 2866005 0.01958134902852014 0.17804970591355207 chr9 141213431 1186956 0.008405404440601687 0.113487118987069 chr10 135534747 1413081 0.010425968478769507 0.13415838370906766 chr11 135006516 1673669 0.012396949788705014 0.13378096001999853 chr12 133851895 1088877 0.008134938993579434 0.10056243185472338 chr13 115169878 811977 0.007050254928636809 0.09286411445244067 chr14 107349540 605350 0.005639055369962461 0.0839585971275376 chr15 102531392 841104 0.008203380287668385 0.10083900485894509 chr16 90354753 973187 0.010770733887126004 0.11672210238256069 chr17 81195210 762038 0.009385258071258144 0.10878497618339708 chr18 78077248 884035 0.011322568643812855 0.15639510124084013 chr19 59128983 674644 0.011409700721556466 0.1530737130653612 chr20 63025520 594330 0.009429989629597662 0.10907811739761183 chr21 48129895 286459 0.0059517894231849045 0.0906655781148084 chr22 51304566 591049 0.011520397619190463 0.119003704881347 chrMT 16571 20675 1.2476615774545894 1.3803773560723376 chrX 155270560 1467616 0.009451991414212714 0.11209371400572563 chrY 59373566 93364 0.0015724842937680382 0.06170010279992627