BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716591.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 = 578,673 number of mapped reads = 499,214 (86.27%) number of supplementary alignments = 2,356 (0.41%) number of secondary alignments = 0 number of mapped bases = 28,666,534 bp number of sequenced bases = 28,658,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,586 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6297 >>>>>>> ACTG content number of A's = 7,349,437 bp (25.65%) number of C's = 5,720,440 bp (19.96%) number of T's = 8,833,902 bp (30.83%) number of G's = 6,753,994 bp (23.57%) number of N's = 377 bp (0%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 144,348 number of insertions = 1,893 mapped reads with insertion percentage = 0.38% number of deletions = 5,348 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.47% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 0.1153X There is a 0.88% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2345432 0.009409934429009907 0.16660901432801345 chr2 243199373 2417502 0.009940412140782945 0.14108472558168683 chr3 198022430 1908322 0.009636898203905488 0.10187369033221022 chr4 191154276 1805906 0.009447374329204124 0.10323137309925376 chr5 180915260 1721958 0.009518036234201582 0.1012870334896919 chr6 171115067 1656504 0.009680643727299595 0.10812071012422213 chr7 159138663 1564210 0.00982922672914501 0.12858444061512575 chr8 146364022 1442450 0.009855222480836172 0.10994471349526479 chr9 141213431 1191646 0.008438616578900346 0.10214944772734191 chr10 135534747 1389185 0.010249659447108423 0.11625703491303795 chr11 135006516 1292589 0.009574271215176015 0.10940116790244997 chr12 133851895 1297853 0.009696186968440006 0.10279823092161755 chr13 115169878 880118 0.007641911368526413 0.09103331450039022 chr14 107349540 867228 0.008078544165163633 0.09426401660849186 chr15 102531392 831664 0.008111310924170424 0.09341745133999797 chr16 90354753 838683 0.00928211269638466 0.10150329471177127 chr17 81195210 802928 0.009888859207335014 0.10551881848502986 chr18 78077248 739417 0.009470326105756186 0.1333082380244513 chr19 59128983 621277 0.010507148414847588 0.14139179603566335 chr20 63025520 609441 0.009669749650617718 0.10230543841863829 chr21 48129895 377519 0.007843752827634467 0.09521168494044807 chr22 51304566 347461 0.006772516114842488 0.08561743864624421 chrMT 16571 1476 0.0890712690845453 0.2892613462173915 chrX 155270560 1629482 0.01049446849422067 0.11064558887872711 chrY 59373566 86283 0.0014532224660381693 0.04882296961603692