BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716515.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 = 1,060,922 number of mapped reads = 958,378 (90.33%) number of supplementary alignments = 4,195 (0.4%) number of secondary alignments = 0 number of mapped bases = 55,233,527 bp number of sequenced bases = 55,218,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,218 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8999 >>>>>>> ACTG content number of A's = 14,241,967 bp (25.79%) number of C's = 10,447,136 bp (18.92%) number of T's = 17,618,422 bp (31.91%) number of G's = 12,910,543 bp (23.38%) number of N's = 644 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 276,911 number of insertions = 3,904 mapped reads with insertion percentage = 0.41% number of deletions = 9,602 mapped reads with deletion percentage = 1% homopolymer indels = 41.82% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.1994X There is a 1.65% 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 4529539 0.018172628745426477 0.2583389836023916 chr2 243199373 5389579 0.02216115499606983 0.2175267355842259 chr3 198022430 4782860 0.02415312245183538 0.17888285938448462 chr4 191154276 3162568 0.016544584124291314 0.1402183268829048 chr5 180915260 2757023 0.01523930596014952 0.13074778231042208 chr6 171115067 3056460 0.01786201562250506 0.14885201643771293 chr7 159138663 2754824 0.017310840420972997 0.40655841471372917 chr8 146364022 4709333 0.03217548230534414 0.21993859977751573 chr9 141213431 2288683 0.016207261475007995 0.14962379706526308 chr10 135534747 2599631 0.0191805500621918 0.2932676475664898 chr11 135006516 1584261 0.011734700271800215 0.13700170339434417 chr12 133851895 2518225 0.018813517731669022 0.1647958346279121 chr13 115169878 1424839 0.012371628977500522 0.11586461236996895 chr14 107349540 1736067 0.016172095381125993 0.13514990267067067 chr15 102531392 1258857 0.01227777147510101 0.12120419740287085 chr16 90354753 1585433 0.01754675816556103 0.15050085459306234 chr17 81195210 2126522 0.026190239547382168 0.17503404871345346 chr18 78077248 1348363 0.017269602022858183 0.22012071894589325 chr19 59128983 1024303 0.01732319664622001 0.26020008150266455 chr20 63025520 1202728 0.01908319042825827 0.15848434343937473 chr21 48129895 549697 0.011421113634259954 0.11479726760277564 chr22 51304566 742781 0.014477873177993553 0.12667752410653085 chrMT 16571 20218 1.2200832780158108 1.2234319544955063 chrX 155270560 1965492 0.012658497528443254 0.13802488821152847 chrY 59373566 115241 0.0019409479295887332 0.05592266767107666