BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524778.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 = 2,467,652 number of mapped reads = 2,231,613 (90.43%) number of supplementary alignments = 9,948 (0.4%) number of secondary alignments = 0 number of mapped bases = 126,769,411 bp number of sequenced bases = 126,730,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,750 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7441 >>>>>>> ACTG content number of A's = 32,267,227 bp (25.46%) number of C's = 22,214,303 bp (17.53%) number of T's = 42,433,218 bp (33.48%) number of G's = 29,812,748 bp (23.52%) number of N's = 2,627 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 642,593 number of insertions = 9,140 mapped reads with insertion percentage = 0.41% number of deletions = 25,052 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.041X std coverageData = 0.398X There is a 3.61% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10685407 0.04287013190631128 0.7193584797361124 chr2 243199373 10999251 0.04522729998979068 0.5373073088816396 chr3 198022430 9162825 0.046271652155768415 0.24467083388368202 chr4 191154276 9008754 0.04712818456648074 0.25201359459668676 chr5 180915260 5754355 0.031806907830771156 0.20004504948589782 chr6 171115067 7550021 0.04412247929049988 0.27756605912949184 chr7 159138663 9239860 0.05806169177128251 0.7698407005076947 chr8 146364022 7003590 0.04785048883119651 0.36133198346004386 chr9 141213431 5004554 0.03543964596398766 0.28043506872452967 chr10 135534747 8230998 0.06072979942184125 0.42118793340893457 chr11 135006516 5568261 0.04124438704869623 0.2922545812295977 chr12 133851895 5493983 0.04104523884402234 0.2294935019766168 chr13 115169878 3956995 0.03435789868597412 0.20926273682868166 chr14 107349540 2818336 0.026253824655420043 0.1892496257406292 chr15 102531392 3302874 0.032213295221818504 0.21529219046100614 chr16 90354753 3586300 0.03969132647620652 0.25027386971884946 chr17 81195210 2010058 0.024755869219378827 0.18331335395777837 chr18 78077248 2681141 0.034339594038970224 0.5249999425550627 chr19 59128983 2243008 0.037934154896592756 0.5115952888701925 chr20 63025520 1794130 0.02846672268630231 0.19337107085352337 chr21 48129895 2014254 0.041850371790755 0.2347087808125568 chr22 51304566 1224959 0.02387621795689686 0.17179088753595673 chrMT 16571 131715 7.948524530806831 5.042010007707244 chrX 155270560 6964893 0.044856494366993974 0.2684212238921658 chrY 59373566 338889 0.0057077420615093254 0.12897701982211135