BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173964.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,858,742 number of mapped reads = 4,761,912 (98.01%) number of supplementary alignments = 637,066 (13.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,379,344 number of mapped paired reads (second in pair) = 2,382,568 number of mapped paired reads (both in pair) = 4,699,472 number of mapped paired reads (singletons) = 62,440 number of mapped bases = 541,385,300 bp number of sequenced bases = 541,029,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,838,201 duplication rate = 65.06% >>>>>>> Insert size mean insert size = 1,284,709.6627 std insert size = 10,008,860.7304 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 52.6071 >>>>>>> ACTG content number of A's = 162,163,009 bp (29.97%) number of C's = 106,796,156 bp (19.74%) number of T's = 160,972,680 bp (29.75%) number of G's = 111,093,866 bp (20.53%) number of N's = 4,112 bp (0%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 4,473,564 number of insertions = 59,071 mapped reads with insertion percentage = 1.19% number of deletions = 145,915 mapped reads with deletion percentage = 2.99% homopolymer indels = 41.48% >>>>>>> Coverage mean coverageData = 0.1749X std coverageData = 3.1077X There is a 3.77% of reference with a coverageData >= 1X There is a 2.82% of reference with a coverageData >= 2X There is a 2.11% of reference with a coverageData >= 3X There is a 1.7% of reference with a coverageData >= 4X There is a 1.28% of reference with a coverageData >= 5X There is a 1.05% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.68% of reference with a coverageData >= 8X There is a 0.51% of reference with a coverageData >= 9X There is a 0.45% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 44830670 0.17986181867928025 1.6016706651644124 chr2 243199373 50666953 0.2083350478045846 9.893091157384307 chr3 198022430 37460266 0.18917183270602225 1.316621723648777 chr4 191154276 36960508 0.19335433542695116 1.6435921946017944 chr5 180915260 33847534 0.18709054172655198 1.30270235407345 chr6 171115067 32037251 0.18722635920774877 1.421025799035855 chr7 159138663 29887272 0.18780647918350302 1.5315719192708117 chr8 146364022 27653963 0.1889396220609461 1.9133576628361106 chr9 141213431 23345047 0.16531746898777638 1.530179124639215 chr10 135534747 26180555 0.1931648937227883 1.8871442020404054 chr11 135006516 24565142 0.18195523244226228 1.3064413739854723 chr12 133851895 24643190 0.18410789029172878 1.3307024075400067 chr13 115169878 17715561 0.15382113194562905 1.1911197974975334 chr14 107349540 16529741 0.15398054803029432 1.177976640566506 chr15 102531392 15117695 0.14744455044558452 1.164976478666727 chr16 90354753 16255354 0.17990590932167122 1.5036400923323463 chr17 81195210 14299797 0.17611626350864787 1.2936842700927424 chr18 78077248 14381553 0.18419646399422274 1.9337523012430735 chr19 59128983 10137416 0.17144580349031202 1.3794637095435698 chr20 63025520 11306363 0.17939341079613463 1.3029151264238878 chr21 48129895 7439380 0.15456879762567527 1.4892299360536458 chr22 51304566 6469832 0.12610635864262063 1.2281326358444582 chrMT 16571 656327 39.606963973206206 35.651818085235085 chrX 155270560 15069855 0.09705545597310913 0.933751594302018 chrY 59373566 3928075 0.06615865046744876 1.1665307555863649