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
A1 F21 I0 R2	308	27.9	1975068	96.7%	1909890	67.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,096,084	G→A	16.9%	E160E (GAG→GAA)	hisB →	fused histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,096,084	0	G	A	16.9%	194.0 / 28.5	77	E160E (GAG→GAA)	hisB	fused histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase
Reads supporting (aligned to +/- strand): ref base G (39/25); new base A (7/6); total (46/31)
Fisher's exact test for biased strand distribution p-value = 7.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

ACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCA  >  W3110S.gb/2096034‑2096140

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:1844921/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:1795941/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:1716765/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:1644255/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:1207349/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:815117/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:739340/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:1243744/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCg                                      >  1:146780/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCg                                      >  1:1746894/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCg                                      >  1:1600552/1‑71 (MQ=255)

aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCg                                      >  1:900347/1‑71 (MQ=255)

 cTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGt                                     <  1:99831/71‑1 (MQ=255)

 cTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGt                                     <  1:1969949/71‑1 (MQ=255)

 cTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGt                                     <  1:1546381/71‑1 (MQ=255)

 cTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGt                                     <  1:790127/71‑1 (MQ=255)

 cTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGt                                     <  1:811043/71‑1 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTa                                   >  1:957438/1‑70 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTAc                                  >  1:747040/1‑71 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTAc                                  >  1:107376/1‑71 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTAc                                  >  1:1101245/1‑71 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTAc                                  >  1:959218/1‑71 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTAc                                  >  1:171483/1‑71 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTAc                                  >  1:1125868/1‑71 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTAc                                  >  1:738869/1‑71 (MQ=255)

    gTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTAc                                  >  1:1407523/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGt                       >  1:858560/1‑70 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:399916/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:537020/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:345624/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:774785/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:992591/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:1055725/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:1833907/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:1109546/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:1202389/1‑71 (MQ=255)

                aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTg                      >  1:106408/1‑71 (MQ=255)

                   gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGt                   <  1:780306/71‑1 (MQ=255)

                   gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGt                   <  1:86377/71‑1 (MQ=255)

                   gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGt                   <  1:1496293/71‑1 (MQ=255)

                   gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGt                   <  1:343203/71‑1 (MQ=255)

                   gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGt                   <  1:1230032/71‑1 (MQ=255)

                   gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGt                   <  1:1761072/71‑1 (MQ=255)

                   gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGt                   <  1:1894851/71‑1 (MQ=255)

                   gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACCTAGTGCGt                   <  1:652798/71‑1 (MQ=255)

                      aaaCCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTg                                          <  1:237350/45‑1 (MQ=255)

                      aaaCCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTg                                          <  1:1309703/45‑1 (MQ=255)

                      aaaCCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTg                                          <  1:231866/45‑1 (MQ=255)

                      aaaCCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTg                                          <  1:227000/45‑1 (MQ=255)

                      aaaCCCTGAACTGGCCAATGATTGGCGAG‑AACTCACCAGACGTg                                          <  1:1031297/44‑1 (MQ=39)

                        aCCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATAc              >  1:996350/1‑71 (MQ=255)

                        aCCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATAc              >  1:965017/1‑71 (MQ=255)

                        aCCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATAc              >  1:41888/1‑71 (MQ=255)

                        aCCCTGAACTGGCAAATGATTGGCGAACAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATAc              >  1:115180/1‑71 (MQ=255)

                             gAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGTCCGt                                     <  1:1951264/43‑1 (MQ=255)

                                   gCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACg    <  1:238819/70‑1 (MQ=255)

                                   gCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACg    <  1:1154778/70‑1 (MQ=255)

                                   gCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACg    <  1:288772/70‑1 (MQ=255)

                                    ccAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCa  <  1:1211768/71‑1 (MQ=255)

                                    ccAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCa  <  1:984339/71‑1 (MQ=255)

                                    ccAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCa  <  1:225849/71‑1 (MQ=255)

                                       aTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAaga        <  1:943855/62‑1 (MQ=255)

                                       aTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAaga        <  1:185535/62‑1 (MQ=255)

                                       aTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAaga        <  1:1291714/62‑1 (MQ=255)

                                       aTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAaga        <  1:1521956/62‑1 (MQ=255)

                                       aTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAaga        <  1:48031/62‑1 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAagag       >  1:1387550/1‑61 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:802706/1‑62 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:929901/1‑62 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:1490835/1‑62 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:959012/1‑62 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:1670854/1‑62 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:385476/1‑62 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:373292/1‑62 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:371999/1‑62 (MQ=255)

                                         gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAgaga      >  1:1726129/1‑62 (MQ=255)

                                               cGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAaga        <  1:964681/54‑1 (MQ=255)

ACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCA  >  W3110S.gb/2096034‑2096140

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A