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
A7 F1 I1 R1	776	60.0	3074904	90.1%	2770488	104.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,111,150	G→A	A276V (GCG→GTG)	rfbD ←	dTDP‑L‑rhamnose synthase, NAD(P)‑dependent dTDP‑4‑dehydrorhamnose reductase subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,111,150	0	G	A	98.2%	179.3 / ‑3.9	56	A276V (GCG→GTG)	rfbD	dTDP‑L‑rhamnose synthase, NAD(P)‑dependent dTDP‑4‑dehydrorhamnose reductase subunit
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (25/30); minor base T (1/0); total (26/30)
Fisher's exact test for biased strand distribution p-value = 4.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TTTCATTTCATCATTCCTTTTAATTCATCTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCGCAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCAAGGGGAATGCCTGCTTTGCGCGCC  >  NC_000913/2111014‑2111278

tttcatttcaTCATTCCTTTTAATTCATCTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGcaca                                                                                                                                >  1:528343/1‑139 (MQ=255)

tttcatttcaTCATTCCTTTTAATTCATCTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGcaca                                                                                                                                >  2:170675/1‑139 (MQ=255)

          tcatTCCTTTTAATTCATCTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTctgct                                                                                                                      >  1:618129/1‑139 (MQ=255)

           catTCCTTTTAATTCATCTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTctgctg                                                                                                                     <  2:340194/139‑1 (MQ=255)

                   ttAATTCATCTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAAttttt                                                                                                             <  2:618129/139‑1 (MQ=255)

                     aaTTCATCTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCt                                                                                                           <  1:880248/139‑1 (MQ=255)

                            cTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTaa                                                                                                    >  1:855374/1‑139 (MQ=255)

                               gCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGc                                                                                                 >  2:1076254/1‑139 (MQ=255)

                               gCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGCCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGc                                                                                                 <  1:1464115/139‑1 (MQ=255)

                                cTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCg                                                                                                >  2:742628/1‑139 (MQ=255)

                                 tCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCga                                                                                               <  1:572834/139‑1 (MQ=255)

                                   caccaTCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCgaga                                                                                             <  1:170675/139‑1 (MQ=255)

                                    accaTCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGcaca                                                                                                                                <  2:879537/103‑1 (MQ=255)

                                    accaTCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGcaca                                                                                                                                >  1:879537/1‑103 (MQ=255)

                                     ccaTCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAAttttt                                                                                                             >  2:1237060/1‑121 (MQ=255)

                                     ccaTCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAAttttt                                                                                                             <  1:966590/121‑1 (MQ=255)

                                     ccaTCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAAttttt                                                                                                             <  1:1237060/121‑1 (MQ=255)

                                     ccaTCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAAttttt                                                                                                             >  2:966590/1‑121 (MQ=255)

                                      caTCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGtt                                                                                          <  1:1124101/139‑1 (MQ=255)

                                         cACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAgg                                                                                                  <  1:232528/128‑1 (MQ=255)

                                         cACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAgg                                                                                                  >  2:232528/1‑128 (MQ=255)

                                             aaCAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGga                                                                                   <  1:1076254/139‑1 (MQ=255)

                                                  gATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGacgacg                                                                              >  2:308384/1‑139 (MQ=255)

                                                   aTGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGAcgacga                                                                             >  1:301024/1‑139 (MQ=255)

                                                    tGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAg                                                                            <  1:308384/139‑1 (MQ=255)

                                                    tGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAg                                                                            <  1:188678/139‑1 (MQ=255)

                                                       aaaaaCTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAAttttt                                                                                                             <  2:830838/103‑1 (MQ=255)

                                                       aaaaaCTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAAttttt                                                                                                             >  1:830838/1‑103 (MQ=255)

                                                         aaaCTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGgt                                                                       <  2:615718/139‑1 (MQ=255)

                                                              aTTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAGAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGgt                                                                       >  1:1335508/1‑134 (MQ=255)

                                                              aTTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAGAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGgt                                                                       <  2:1335508/134‑1 (MQ=255)

                                                              aTTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTAtt                                                                                                      >  1:387811/1‑103 (MQ=255)

                                                              aTTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTAtt                                                                                                      <  2:387811/103‑1 (MQ=255)

                                                              aTTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAgg                                                                  >  1:1073132/1‑139 (MQ=255)

                                                               ttAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGa                                                                 >  1:997328/1‑139 (MQ=255)

                                                                     tGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCt                                                           <  1:742628/139‑1 (MQ=255)

                                                                       cTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAg                                                                            >  1:1521594/1‑120 (MQ=255)

                                                                       cTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAg                                                                            <  2:1521594/120‑1 (MQ=255)

                                                                       cTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCtgt                                                         >  1:1217473/1‑139 (MQ=255)

                                                                       cTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCtgt                                                         >  2:1201980/1‑139 (MQ=255)

                                                                               gTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTa                                                 <  2:1217473/139‑1 (MQ=255)

                                                                                     aatTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGt                                           <  2:1073132/139‑1 (MQ=255)

                                                                                       ttCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAg                                                                            >  1:483185/1‑104 (MQ=255)

                                                                                       ttCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAg                                                                            <  2:483185/104‑1 (MQ=255)

                                                                                            tGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCTCAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCtt                                    >  1:1453588/1‑139 (MQ=255)

                                                                                               gCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCttgtt                                 <  2:528343/139‑1 (MQ=255)

                                                                                               gCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCttgtt                                 <  2:301024/139‑1 (MQ=255)

                                                                                                cATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGtt                                                                                                                           <  1:1509281/48‑1 (MQ=255)

                                                                                                cATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGtt                                                                                                                           >  2:1509281/1‑48 (MQ=255)

                                                                                                    cGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAg                                                                                                                             >  2:1497620/1‑42 (MQ=255)

                                                                                                    cGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAg                                                                                                                             <  1:1497620/42‑1 (MQ=255)

                                                                                                        tCACGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGCTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTTGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCCAg                        >  2:1154167/1‑139 (MQ=255)

                                                                                                          aCGCCAACCTGCCAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCAAggg                      >  1:667837/1‑139 (MQ=255)

                                                                                                                     ccAGTCAGGCAAGACAAGCACCAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCAAGGGGAATGCCTGCt           >  1:675215/1‑139 (MQ=255)

                                                                                                                     ccAGTCAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCAAGGGGAATGCCTGCt           >  1:1118402/1‑139 (MQ=255)

                                                                                                                          cAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCAAGGGGAATGCCTGCTTTgcg      <  2:667837/139‑1 (MQ=255)

                                                                                                                          cAGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCAAGGGGAATGCCTGCTTTgcg      <  1:1201980/139‑1 (MQ=255)

                                                                                                                           aGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCt                                                           >  1:1406329/1‑85 (MQ=255)

                                                                                                                           aGGCAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCt                                                           <  2:1406329/85‑1 (MQ=255)

                                                                                                                              cAAGACAAGCACAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCAAGGGGAATGCCTGCTTTGCGCGcc  <  2:997328/139‑1 (MQ=255)

TTTCATTTCATCATTCCTTTTAATTCATCTTGCTCCACCATCACGAACAAGATGCAAAAACTATTAAATTGCTGTAGTCGTAAATAATTCATTGAGCATTCGTTTCACGCCAACCTGCCAGTCAGGCAAGACAAGCGCAAAGTTCTGCTGAAATTTTTCTGTATTAAGGCGAGAGTTATGTGGACGACGAGCTGGTGTAGGATAGGCTGTTGTTGGTACTGCGTTGAGCTTGTTGAGTGCAAGGGGAATGCCTGCTTTGCGCGCC  >  NC_000913/2111014‑2111278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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