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
A12 F1 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,353,121	C→T	310 (TAG→TAA)	yhcC ←	putative Fe‑S oxidoreductase, Radical SAM superfamily protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,353,121	0	C	T	96.4%	167.1 / ‑1.9	56	310 (TAG→TAA)	yhcC	putative Fe‑S oxidoreductase, Radical SAM superfamily protein
Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (30/24); total (31/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

CATAATACTGCGCCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACCTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCGCCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATCGATTTTCGCACCACAGCGG  >  NC_000913/3352992‑3353234

cATAATACTGCGCCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGtt                                                                                                          <  2:401741/139‑1 (MQ=255)

     taCTGCGCCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAgg                                                                                                     >  1:928217/1‑139 (MQ=255)

     taCTGCGCCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAgg                                                                                                     >  2:169199/1‑139 (MQ=255)

     taCTGCGCCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACCTACTCCGTTGGAgg                                                                                                     >  2:531106/1‑139 (MQ=255)

        tGCGCCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAg                                                                                                  >  1:52400/1‑139 (MQ=255)

          cgcCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAgg                                                                                                     >  2:431019/1‑134 (MQ=255)

          cgcCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAgg                                                                                                     <  1:431019/134‑1 (MQ=255)

          cgcCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGcc                                                                                                >  1:159658/1‑139 (MQ=255)

          cgcCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGcc                                                                                                >  1:1004302/1‑139 (MQ=255)

          cgcCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGcc                                                                                                >  1:40195/1‑139 (MQ=255)

          cgcCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGcc                                                                                                >  1:52302/1‑139 (MQ=255)

          cgcCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGCTGGAGGTAGcc                                                                                                >  2:894563/1‑139 (MQ=255)

           gcCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTTTGACAGTTACGTTTTAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCa                                                                                               >  1:714512/1‑139 (MQ=255)

               gcagACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGa                                                                                           <  2:892715/139‑1 (MQ=255)

                    cGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTcc                                                                                      <  1:169199/139‑1 (MQ=255)

                           gCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAgcacc                                                                               <  2:440821/139‑4 (MQ=255)

                              tCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACCTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCGCCGAt                                                                            <  1:531106/139‑1 (MQ=255)

                                 ttAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCAGTTGGAGGTAGCCACGGACGTCCCAGCACCGATccc                                                                         >  1:824515/1‑139 (MQ=255)

                                     ggAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTa                                                                     >  2:918176/1‑139 (MQ=255)

                                         ttCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGcc                                                                 <  2:1171037/139‑1 (MQ=255)

                                         ttCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGcc                                                                 >  2:329784/1‑139 (MQ=255)

                                         ttCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGcc                                                                 >  2:653564/1‑139 (MQ=255)

                                          tCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCa                                                                <  1:1297434/139‑1 (MQ=255)

                                            cTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGa                                                                             <  1:31065/124‑1 (MQ=255)

                                            cTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGa                                                                             >  2:31065/1‑124 (MQ=255)

                                              tCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGTAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGtt                                                            <  2:928217/139‑1 (MQ=255)

                                              tCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGtt                                                            <  1:653564/139‑1 (MQ=255)

                                                 cGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGttcat                                                         >  2:103724/1‑139 (MQ=255)

                                                                  aataCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGc                                        <  2:1004302/139‑1 (MQ=255)

                                                                    taCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACt                                                                                                               <  1:484910/66‑1 (MQ=255)

                                                                    taCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACt                                                                                                               >  2:484910/1‑66 (MQ=255)

                                                                     aCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGGGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGc                                                                  <  1:619911/110‑1 (MQ=255)

                                                                     aCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGGGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGc                                                                  >  2:619911/1‑110 (MQ=255)

                                                                     aCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGttcat                                                         <  2:139806/119‑1 (MQ=255)

                                                                     aCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGttcat                                                         >  1:139806/1‑119 (MQ=255)

                                                                     aCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCg                                     >  2:699311/1‑139 (MQ=255)

                                                                     aCCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCg                                     >  2:651284/1‑139 (MQ=255)

                                                                       ccAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGAc                                   <  1:918176/139‑1 (MQ=255)

                                                                         aaTTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCa                                 >  2:786971/1‑139 (MQ=255)

                                                                                     tACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATc                     >  2:724055/1‑139 (MQ=255)

                                                                                          tataAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACt                                                                                                               >  1:200064/1‑44 (MQ=255)

                                                                                          tataAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACt                                                                                                               <  2:200064/44‑1 (MQ=255)

                                                                                            taAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGttcatt                                                        <  2:1251043/97‑1 (MQ=255)

                                                                                            taAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGttcatt                                                        >  1:1251043/1‑97 (MQ=255)

                                                                                             aaaTTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATCGATTTTCg             <  2:159658/139‑1 (MQ=255)

                                                                                              aaTTGTGTGAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATCGATTTTCGc            >  2:1116119/1‑139 (MQ=255)

                                                                                                  gtgtgAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATCGATTTTCGcacca        <  1:103724/139‑1 (MQ=255)

                                                                                                   tgtgAGAAATGCGGAATTCCCCTCAACGACTTACt                                                                                                               <  2:279445/35‑1 (MQ=255)

                                                                                                   tgtgAGAAATGCGGAATTCCCCTCAACGACTTACt                                                                                                               >  1:279445/1‑35 (MQ=255)

                                                                                                   tgtgAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGa                                                                                           >  2:347468/1‑55 (MQ=255)

                                                                                                   tgtgAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGa                                                                                           <  1:347468/55‑1 (MQ=255)

                                                                                                   tgtgAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAg                                                 <  2:279656/97‑1 (MQ=255)

                                                                                                   tgtgAGAAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAg                                                 >  1:279656/1‑97 (MQ=255)

                                                                                                        gaAATGCGGAATTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATCGATTTTCGCACCACAGCgg  <  1:651284/139‑1 (MQ=255)

                                                                                                                 aaTTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATCGATTTTCGCACCACAGc    >  2:382945/1‑128 (MQ=255)

                                                                                                                 aaTTCCCCTCAACGACTTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCACCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATCGATTTTCGCACCACAGc    <  1:382945/128‑1 (MQ=255)

CATAATACTGCGCCAGCAGACGAATTTGCTTCATTAGGGAATTCCTTCACGACAACCTGCCCCAATAATACCCAATTCTGACAGTTACGTTATAAATTGTGTGAGAAATGCGGAATTCCCCTCAACGACCTACTCCGTTGGAGGTAGCCACGGACGTCCCAGCGCCGATCCCTGTACGCCATGTTCATTCAGATAGCGATCCAGCTCGACCATTCCCGTCCATCGATTTTCGCACCACAGCGG  >  NC_000913/3352992‑3353234

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A