Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A22 F44 I0 R1	387	90.4	3244086	98.5%	3195424	139.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,640,749	G→T	10.7%	intergenic (‑164/+590)	essQ ← / ← cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,640,749	0	G	T	10.7%	184.9 / 11.0	56	intergenic (‑164/+590)	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
Reads supporting (aligned to +/- strand): ref base G (21/29); new base T (3/3); total (24/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01

GATGGTGCAATATGTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCAAGAGTCAGAACACAGTTTTTCA  >  NC_000913/1640607‑1640897

gATGGTGCAATATGTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAAt                                                                                                                                                <  1:597937/149‑1 (MQ=255)

     tGCAATATGTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGtttt                                                                                                                                           <  2:329497/149‑1 (MQ=255)

      gCAATATGTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTc                                                                                                                                          <  2:621317/149‑1 (MQ=255)

      gCAATATGTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTc                                                                                                                                          <  4:420039/149‑1 (MQ=255)

          tatGTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAACAATACGAGAAATGTTTTCatat                                                                                                                                      >  3:665866/1‑149 (MQ=255)

             gTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAAt                                                                                                                                                <  2:286951/136‑1 (MQ=255)

             gTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAAt                                                                                                                                                >  1:286951/1‑136 (MQ=255)

             gTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTa                                                                                                                                   <  3:746968/149‑1 (MQ=255)

              tttGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAg                                                                                                                                  <  2:50982/149‑1 (MQ=255)

                 gAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAgtgt                                                                                                                               >  1:148738/1‑149 (MQ=255)

                  aaaaGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACAGACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTa                                                                                                                              >  4:463110/1‑149 (MQ=255)

                  aaaaGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTATTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTa                                                                                                                              <  1:207542/149‑1 (MQ=255)

                   aaaGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTAc                                                                                                                             <  2:572052/149‑1 (MQ=255)

                    aaGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACt                                                                                                                            <  1:767137/149‑1 (MQ=255)

                        tCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGtat                                                                                                                        <  1:32957/149‑1 (MQ=255)

                               cTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCa                                                                                                                 <  4:678226/149‑1 (MQ=255)

                                tACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCAt                                                                                                                >  3:510535/1‑149 (MQ=255)

                                   ggggTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTta                                                                                                             >  4:513102/1‑149 (MQ=255)

                                    gggTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGaa                                                                                                                                                  <  3:266023/111‑1 (MQ=255)

                                    gggTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGaa                                                                                                                                                  >  4:266023/1‑111 (MQ=255)

                                        aGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAg                                                                                                        <  4:510535/149‑1 (MQ=255)

                                          ttttGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTa                                                                                                                                   <  1:481232/120‑1 (MQ=255)

                                          ttttGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTa                                                                                                                                   >  2:481232/1‑120 (MQ=255)

                                          ttttGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGa                                                                                                      >  1:329778/1‑149 (MQ=255)

                                                   cacaCGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTAt                                                                                             <  2:593500/149‑1 (MQ=255)

                                                         ttgttCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGa                                                                                       >  1:267356/1‑149 (MQ=255)

                                                          tgttCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGaa                                                                                      <  2:148738/149‑1 (MQ=255)

                                                               tcAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTaa                                                                                 >  1:323510/1‑149 (MQ=255)

                                                                 aaCGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACTAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAAc                                                                                     <  1:201989/143‑1 (MQ=255)

                                                                 aaCGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACTAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAAc                                                                                     >  4:186357/1‑143 (MQ=255)

                                                                 aaCGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACTAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAAc                                                                                     <  1:80439/143‑1 (MQ=255)

                                                                 aaCGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACTAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAAc                                                                                     <  3:186357/143‑1 (MQ=255)

                                                                 aaCGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACTAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAAc                                                                                     >  2:80439/1‑143 (MQ=255)

                                                                 aaCGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATTTCAGAACGTaaaa                                                                               >  2:709752/1‑149 (MQ=255)

                                                                 aaCGGCGCTAAAAAAACATACACATGAAAAATGTGGGTAATTATTTTGAAAGAAAGCCATATATAAAATAATAATACTAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAAc                                                                                     >  2:201989/1‑143 (MQ=255)

                                                                   cGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAAc                                                                             <  2:301492/149‑1 (MQ=255)

                                                                       gcTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCaa                                                                         <  3:513102/149‑1 (MQ=255)

                                                                         tAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCaaaa                                                                       >  2:706859/1‑149 (MQ=255)

                                                                         tAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCaaaa                                                                       >  3:791265/1‑149 (MQ=255)

                                                                         tAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCaaaa                                                                       <  3:463110/149‑1 (MQ=255)

                                                                              aaaCATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACg                                                                  >  4:737556/1‑149 (MQ=255)

                                                                                        aTTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTAt                                                        <  4:803750/149‑1 (MQ=255)

                                                                                         ttAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTAtc                                                       <  1:709752/149‑1 (MQ=255)

                                                                                          tAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTAtct                                                      <  1:788539/149‑1 (MQ=255)

                                                                                                       aaTTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTc                                          <  3:236318/148‑1 (MQ=255)

                                                                                                       aaTTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTc                                          >  4:236318/1‑148 (MQ=255)

                                                                                                         ttattTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTg                                       >  4:673244/1‑149 (MQ=255)

                                                                                                           attTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGcc                                     >  1:730914/1‑149 (MQ=255)

                                                                                                                     aaagTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCAc                           <  2:329778/149‑1 (MQ=255)

                                                                                                                       agTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCAccc                         <  3:673244/149‑1 (MQ=255)

                                                                                                                         tCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCaa                       >  2:503295/1‑149 (MQ=255)

                                                                                                                           atatatAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCAaga                     <  2:267356/149‑1 (MQ=255)

                                                                                                                                         aataCGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCAAGAGTCAGAACACAGtt       <  1:706859/149‑1 (MQ=255)

                                                                                                                                          ataCGAGAAATGTTTTCATATTTAGTGTACTGTATACGACCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCAAGAGTCAGAACACAGttt      >  1:579868/1‑149 (MQ=255)

                                                                                                                                           taCGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCAAGAGTCAGAACACAGtttt     >  1:734238/1‑149 (MQ=255)

                                                                                                                                             cGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCAAGAGTCAGAACACAGTTTTTc   <  4:791265/149‑1 (MQ=255)

                                                                                                                                              gagaAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCAAGAGTCAGAACACAGTTTTTCa  >  2:563097/1‑149 (MQ=255)

GATGGTGCAATATGTTTGAAAAGATCGGAGTCTACGGGGTAGTTTTGACAGCACACGTTGTTCTCAACGGCGCTAAAAAAACATACACATTAAAAATGTGGGTAATTATTTTGAAAGAAAGTCATATATAAAATAATAATACGAGAAATGTTTTCATATTTAGTGTACTGTATACGGCCATTTATACAGGAAAAGCCTATGTCAGAACGTAAAAACTCAAAATCACGCCGTAATTATCTCGTTAAATGTTCCTGCCCAAACTGCACCCAAGAGTCAGAACACAGTTTTTCA  >  NC_000913/1640607‑1640897

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A