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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,280,578	C→T	48.6%	L13L (CTG→CTA)	yijD ←	conserved inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,280,578	0	C	T	48.6%	5.5 / 99.4	111	L13L (CTG→CTA)	yijD	conserved inner membrane protein
Reads supporting (aligned to +/- strand): ref base C (27/30); new base T (29/25); total (56/55)
Fisher's exact test for biased strand distribution p-value = 5.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.45e-01

Only 100 of 130 total aligned reads displayed.

GAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTCCTTCACATTTCCCGGAAT  >  minE/2280510‑2280642

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:1804315/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:10493/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:2762313/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:2667599/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:1185847/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:802865/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:2608296/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:2208257/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:2566257/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:2521573/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:824722/1‑69 (MQ=255)

gAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGcc                                                                  >  1:241061/1‑69 (MQ=255)

          caATTGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:2896005/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:3221436/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:1435953/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:1483185/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:1498694/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:1510179/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:495716/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:172302/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:1955056/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:1918405/69‑1 (MQ=255)

          caATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:943378/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCg                                                        <  1:211044/68‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:3300451/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:33726/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:3169657/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:3412678/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:2868306/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:1031207/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:808108/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:858993/69‑1 (MQ=255)

           aaTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:136292/69‑1 (MQ=255)

            aTGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:2552927/68‑1 (MQ=255)

             tGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:293890/67‑1 (MQ=255)

              ggAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGt                                                       <  1:1883398/66‑1 (MQ=255)

               gAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTAcc                                                    >  1:1757709/1‑68 (MQ=255)

               gAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTAcc                                                    >  1:1063474/1‑68 (MQ=255)

               gAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTAcc                                                    >  1:2944809/1‑68 (MQ=255)

               gAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTAcc                                                    >  1:2100903/1‑68 (MQ=255)

               gAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTAcc                                                    >  1:1273204/1‑68 (MQ=255)

                       cAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTg                                           >  1:791180/1‑69 (MQ=255)

                       cAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTg                                           >  1:2705041/1‑69 (MQ=255)

                       cAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTg                                           >  1:1517315/1‑69 (MQ=255)

                                      aCCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGAt                                         >  1:236955/1‑56 (MQ=255)

                                      aCCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:3319149/1‑69 (MQ=255)

                                      aCCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:1548425/1‑69 (MQ=255)

                                      aCCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:2857718/1‑69 (MQ=255)

                                      aCCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:306800/1‑69 (MQ=255)

                                      aCCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGACTTGCTTGTTTCAt                            >  1:1618946/1‑69 (MQ=255)

                                                  tAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCTTTACTCGTCCt                  >  1:220759/1‑67 (MQ=255)

                                                  tAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTccat                 >  1:1564809/1‑66 (MQ=255)

                                                  tAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTCCtt                 >  1:1128353/1‑68 (MQ=255)

                                                  tAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTCCtt                 >  1:1695095/1‑68 (MQ=255)

                                                    aGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTCCTTcac              <  1:1410981/69‑1 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCa                             >  1:1396822/1‑53 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCa                             >  1:376978/1‑53 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:1042836/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:3319292/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:753360/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:806099/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:599267/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:3080939/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:933650/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:3399730/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:3350169/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:2704263/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:2009376/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:2051377/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:2240707/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:180232/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:172758/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:2382975/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:2513621/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:1280451/1‑54 (MQ=255)

                                                     gCCAGCAACCAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:2658996/1‑54 (MQ=255)

                                                     gCCAGCAACAAACGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCAt                            >  1:3149676/1‑54 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:1302578/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:1374028/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:860071/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:1640077/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:1237900/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:2777487/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:194286/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:1943042/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:648407/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:949796/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:52007/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:2009463/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:2083858/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:228569/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:2295751/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:2339110/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:2578779/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:3141152/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:3139124/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:2598593/51‑1 (MQ=255)

                                                          caaccaacGCTAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTa                          <  1:2654709/51‑1 (MQ=255)

                                                                  gCCAGCAGCAGCTTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTCCTTCACATTTCCCGGaat  <  1:3224963/67‑1 (MQ=255)

                                                                   ccAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTCCTTCACATTTCCCGGaat  <  1:2129421/66‑1 (MQ=255)

GAAAATGGCACAATGGAGCTAAACAGCGCTGCGAAAGTACCATTAATCGATAAGCCAGCAACTAACGCCAGCAGCAGCGTACCTCTATCTTGATTTGCTTGTTTCATTACTCGTCCTTCACATTTCCCGGAAT  >  minE/2280510‑2280642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A