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 F28 I1 R1	252	48.5	1661298	98.8%	1641362	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,612,137	T→C	Y80H (TAT→CAT)	hyfR →	DNA‑binding transcriptional activator HyfR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,612,137	0	T	C	90.6%	150.8 / 5.4	53	Y80H (TAT→CAT)	hyfR	DNA‑binding transcriptional activator HyfR
Reads supporting (aligned to +/- strand): ref base T (2/3); new base C (26/22); total (28/25)
Fisher's exact test for biased strand distribution p-value = 6.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTATTACGCGCCTTCATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGTATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGCACACTGTTTAACTGGCTGGCGCG  >  NC_000913/2612008‑2612273

ttattaCGCGCCTTCATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCga                                                                                                                                <  1:136354/140‑1 (MQ=255)

      cgcgCCTTCATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCgag                                                                                                                               >  2:617860/1‑135 (MQ=255)

      cgcgCCTTCATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCgag                                                                                                                               <  1:617860/135‑1 (MQ=255)

        cgcCTTCATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGCTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGTATCAGGGCGAGATGGTCg                                                                                                                        >  1:68384/1‑140 (MQ=255)

             tCATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGAt                                                                                                                             >  2:382691/1‑130 (MQ=255)

             tCATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGAt                                                                                                                             <  1:382691/130‑1 (MQ=255)

              cATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGCTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGTATCAGGGCGAGATGGTCGattatt                                                                                                                  <  2:68384/140‑1 (MQ=255)

                     cTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCa                                                                                                           >  2:756092/1‑140 (MQ=255)

                                           tACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCagtagt                                                                                     >  2:163049/1‑140 (MQ=255)

                                                     tGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCgg                                                                           >  1:540637/1‑140 (MQ=255)

                                                     tGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCATTCTCGGCAGTAGTGGAATGGCgg                                                                           >  2:336405/1‑140 (MQ=255)

                                                         cTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGTATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGGATGGCGGAGCt                                                                       <  1:549339/140‑1 (MQ=255)

                                                          tGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTa                                                                      >  2:217844/1‑140 (MQ=255)

                                                          tGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTa                                                                      >  1:603548/1‑140 (MQ=255)

                                                            cATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGTAGTAGTGGAATGGCGGAGCTACg                                                                    >  1:428882/1‑140 (MQ=255)

                                                             aTGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGc                                                                   <  1:203296/140‑1 (MQ=255)

                                                              tGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCt                                                                  >  1:52585/1‑140 (MQ=255)

                                                                 tctcAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGc                                                                        <  2:115880/131‑1 (MQ=255)

                                                                 tctcAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGc                                                                        >  1:115880/1‑131 (MQ=255)

                                                                 tctcAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTa                                                               >  1:105687/1‑140 (MQ=255)

                                                                    cAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTc                                                            >  1:826381/1‑140 (MQ=255)

                                                                    cAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTc                                                            <  2:105687/140‑1 (MQ=255)

                                                                      aaaGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCg                                                                            <  1:282280/122‑1 (MQ=255)

                                                                      aaaGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCg                                                                            >  2:282280/1‑122 (MQ=255)

                                                                            aCTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCAc                                                    >  2:806510/1‑140 (MQ=255)

                                                                             cTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACg                                                   >  2:63639/1‑140 (MQ=255)

                                                                               tCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGc                                                 <  1:799071/140‑1 (MQ=255)

                                                                                   ttACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTc                                             >  2:306130/1‑140 (MQ=255)

                                                                                        gCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGtttt                                        >  1:406474/1‑140 (MQ=255)

                                                                                         cTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGTATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       >  2:354683/1‑140 (MQ=255)

                                                                                         cTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGTATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       <  1:315814/140‑1 (MQ=255)

                                                                                         cTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       <  1:63639/140‑1 (MQ=255)

                                                                                         cTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       >  2:578375/1‑140 (MQ=255)

                                                                                         cTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       <  2:540637/140‑1 (MQ=255)

                                                                                           aCCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGc                                                 >  2:693585/1‑128 (MQ=255)

                                                                                           aCCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGc                                                 <  1:693585/128‑1 (MQ=255)

                                                                                           aCCATGATGATGGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACt                                     >  1:617924/1‑140 (MQ=255)

                                                                                              atgatgatgGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTcc                                  <  2:790124/140‑1 (MQ=255)

                                                                                                 atgatgGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCa                                <  2:50656/139‑1 (MQ=255)

                                                                                                 atgatgGCAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCa                                >  1:50656/1‑139 (MQ=255)

                                                                                                      ggCAGTGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       >  2:331003/1‑127 (MQ=255)

                                                                                                      ggCAGTGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       <  1:331003/127‑1 (MQ=255)

                                                                                                        cAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGca                        <  2:603548/140‑1 (MQ=255)

                                                                                                        cAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGca                        <  1:306130/140‑1 (MQ=255)

                                                                                                        cAGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGca                        <  1:163049/140‑1 (MQ=255)

                                                                                                         aGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       >  2:809345/1‑124 (MQ=255)

                                                                                                         aGCGATGTGACGGCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTa                                       <  1:809345/124‑1 (MQ=255)

                                                                                                                     gCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGca                        <  2:177826/127‑1 (MQ=255)

                                                                                                                     gCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGca                        >  1:177826/1‑127 (MQ=255)

                                                                                                                     gCAACAACAGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGCACACTGTTTAActg           >  2:539073/1‑140 (MQ=255)

                                                                                                                          aacaGAGCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGCACACTGTTTAActggctgg      <  1:806510/140‑1 (MQ=255)

                                                                                                                              gagCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGTAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGCACACTGTTTAACTGGCTGGcgcg  <  2:428882/140‑1 (MQ=255)

                                                                                                                              gagCATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGCACACTGTTTAACTGGCTGGcgcg  <  1:756092/140‑1 (MQ=255)

TTATTACGCGCCTTCATCCCGCTGCCGCCGCCGTTCAGCCCGGTACAACTTATTGAACTGCATGTTCTCAAAAGCAACTTCTATTACCGCTACCATGATGATGGCAGCGATGTGACGGCAACAACAGAGTATCAGGGCGAGATGGTCGATTATTCGCGTCACGCCGTCCTTCTCGGCAGTAGTGGAATGGCGGAGCTACGCTTTATTCGCACCCACGGCAGTCGTTTTACTTCCCAGGATTGCACACTGTTTAACTGGCTGGCGCG  >  NC_000913/2612008‑2612273

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A