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
A6 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	385,142	A→C	35.2%	I118L (ATC→CTC) ‡	cstA →	carbon starvation protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	385,142	0	A	C	35.2%	31.3 / 53.9	54	I118L (ATC→CTC) ‡	cstA	carbon starvation protein
Reads supporting (aligned to +/- strand): ref base A (14/21); new base C (7/12); total (21/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCATTGCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGC  >  minE/385074‑385211

ccATTGCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATc                                                                     >  1:724685/1‑71 (MQ=255)

      ccGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGgctg                                                               <  1:3752196/71‑1 (MQ=255)

       cGGTGCTGGTCCGCTGGTGGGTCCGGTTCTCGCCGTGCAGATGGGCTACCTGCCTGGCACGCTGTGgctgc                                                              <  1:2802760/71‑1 (MQ=255)

           gCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGgatgat                                                                      >  1:2519884/1‑59 (MQ=255)

           gCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGgatgat                                                                      >  1:3264642/1‑59 (MQ=255)

            cAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCt                                                         <  1:1548247/71‑1 (MQ=255)

                tCCGCTGGTGGGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGcg                                                         >  1:4242236/1‑66 (MQ=255)

                  cGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTAGCTGGggt                                                    <  1:4945212/70‑1 (MQ=255)

                   gCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGggtgg                                                  <  1:2738382/71‑1 (MQ=255)

                    cTGGTGGGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGggtcgt                                                 <  1:3437747/71‑1 (MQ=255)

                       gtggGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGgct                                                                <  1:499600/53‑1 (MQ=255)

                       gtggGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTgct                                              >  1:3439234/1‑71 (MQ=255)

                       gtggGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTgct                                              >  1:449019/1‑71 (MQ=255)

                       gtggGTCCGGTTCGCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGgct                                                                <  1:3781756/53‑1 (MQ=255)

                          ggtccGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGc                                           >  1:3274463/4‑71 (MQ=255)

                           ggCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGcc                                          <  1:5507184/71‑1 (MQ=255)

                                gTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCg                                                           <  1:1648172/49‑1 (MQ=255)

                                 tACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGggtgg                                                  <  1:5656408/57‑1 (MQ=255)

                                 tACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGCCTGCTCGCTGGggtgg                                                  <  1:3690331/57‑1 (MQ=255)

                                  aCTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTgg                                                       >  1:4122070/1‑51 (MQ=255)

                                  aCTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtgcg                                    >  1:4901219/1‑70 (MQ=255)

                                   cTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTtctc                                             >  1:2271265/1‑60 (MQ=255)

                                     ggcggcGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTtctc                                             >  1:3012489/1‑58 (MQ=255)

                                      gcggcgCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtgcggtg                                 >  1:1625793/1‑69 (MQ=255)

                                      gccgcgcAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCcggtgcggt                                  <  1:1569900/65‑1 (MQ=255)

                                      gccgcgcAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCcggtgcggt                                  <  1:12417/65‑1 (MQ=255)

                                         gcgcAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAg                              <  1:2642605/69‑1 (MQ=255)

                                          cgcAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGac                           <  1:4336456/71‑2 (MQ=255)

                                          cgcAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGac                           <  1:3892571/71‑2 (MQ=255)

                                           gcAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAtt                          >  1:5187398/1‑71 (MQ=255)

                                            cagaTGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGActt                         <  1:4055455/68‑1 (MQ=255)

                                            cAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTggg                                                      <  1:1156919/42‑1 (MQ=255)

                                            cAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTggg                                                      <  1:4314084/42‑1 (MQ=255)

                                            cAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAttt                         <  1:1112480/71‑1 (MQ=255)

                                              gaTGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGActtta                       >  1:3683789/2‑69 (MQ=255)

                                              gaTGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGActtta                       <  1:1917284/70‑3 (MQ=255)

                                              gaTGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGActtta                       <  1:5612495/70‑3 (MQ=255)

                                              aaTGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGtggtgg                                                  <  1:4952236/44‑1 (MQ=255)

                                              aaTGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGggtgg                                                  <  1:890215/44‑1 (MQ=255)

                                                tGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATg                     <  1:4973445/71‑1 (MQ=255)

                                                tGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTAGCCGGTGCGGTGCAGGATTTCATg                     >  1:5038970/1‑71 (MQ=255)

                                                     tACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATGGTGCt                >  1:268300/1‑71 (MQ=255)

                                                     tACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATGGTGCt                >  1:2429487/1‑71 (MQ=255)

                                                       ccTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCtgt              <  1:3102020/71‑1 (MQ=255)

                                                        cTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCtgtt             >  1:4242997/1‑71 (MQ=255)

                                                         tGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcg                                         >  1:5497278/1‑42 (MQ=255)

                                                         tGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcg                                         >  1:3477614/1‑42 (MQ=255)

                                                           ccGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAttt                         <  1:808785/56‑1 (MQ=255)

                                                           ccGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCtgtttgt          >  1:4970713/1‑71 (MQ=255)

                                                             ggggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCa                       >  1:890358/1‑56 (MQ=255)

                                                             ggggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCa                       >  1:3114377/1‑56 (MQ=255)

                                                              gggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtg                                      <  1:247791/40‑1 (MQ=255)

                                                              gggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtg                                      <  1:4647609/40‑1 (MQ=255)

                                                              gggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtg                                      <  1:4303072/40‑1 (MQ=255)

                                                               ggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCt      <  1:3221073/71‑1 (MQ=255)

                                                               ggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCt      <  1:416204/71‑1 (MQ=255)

                                                                gatgatCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCt      <  1:356398/70‑1 (MQ=255)

                                                                   gatCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTAcgc  >  1:4146158/1‑71 (MQ=255)

                                                                    atCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAttt                         <  1:3721332/47‑1 (MQ=255)

                                                                    atCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAttt                         <  1:3860205/47‑1 (MQ=255)

CCATTGCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGC  >  minE/385074‑385211

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