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 I2 R1	78	65.3	3016648	94.6%	2853749	111.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,901,992	C→T	A77T (GCC→ACC)	bglH ←	carbohydrate‑specific outer membrane porin, cryptic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,901,992	0	C	T	100.0%	161.2 / NA	47	A77T (GCC→ACC)	bglH	carbohydrate‑specific outer membrane porin, cryptic
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (23/24); total (23/24)

CATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGCGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTTCTCTTAACGCCTTTTCTAATAA  >  NC_000913/3901857‑3902115

cATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTggtggc                                                                                                                          <  2:1138044/139‑1 (MQ=255)

cATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTggtggc                                                                                                                          <  2:345003/139‑1 (MQ=255)

cATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTggtggc                                                                                                                          <  2:389742/139‑1 (MQ=255)

cATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTggtggc                                                                                                                          <  2:440234/139‑1 (MQ=255)

cATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTggtggc                                                                                                                          <  2:772058/139‑1 (MQ=255)

 aTCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCTGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCa                                                                                                                         <  2:209742/139‑1 (MQ=255)

 aTCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCa                                                                                                                         <  2:845722/139‑1 (MQ=255)

 aTCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCa                                                                                                                         <  2:787429/139‑1 (MQ=255)

  tCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCAt                                                                                                                        >  1:1045264/1‑139 (MQ=255)

        acaAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCtt                                                                                                                  >  1:733444/1‑139 (MQ=255)

        acaAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGG‑TTGGTGGCATACCCTTg                                                                                                                 <  2:1278839/139‑1 (MQ=255)

         caAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTg                                                                                                                 <  1:523944/139‑1 (MQ=255)

                 cTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCg                                                                                                         <  1:25081/139‑1 (MQ=255)

                         tttCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACg                                                                                                 <  1:284835/139‑1 (MQ=255)

                         tttCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACg                                                                                                 <  2:1045264/139‑1 (MQ=255)

                                         gaaTAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCg                                                                                 <  2:765474/139‑1 (MQ=255)

                                         gaaTAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCg                                                                                 >  2:1013084/1‑139 (MQ=255)

                                          aaTAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATa                                                                                                                       <  1:1464624/100‑1 (MQ=255)

                                          aaTAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATa                                                                                                                       >  2:1464624/1‑100 (MQ=255)

                                               aTCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCa                                                                                                                         <  2:106905/93‑1 (MQ=255)

                                               aTCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCa                                                                                                                         >  1:106905/1‑93 (MQ=255)

                                               aTCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCg                                                                           <  1:1013084/139‑1 (MQ=255)

                                                  gAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGtat                                                                        <  1:1070539/139‑1 (MQ=255)

                                                   aGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCg                                                                                 >  1:159618/1‑129 (MQ=255)

                                                   aGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCg                                                                                 <  2:159618/129‑1 (MQ=255)

                                                    gCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGc                                                                                                <  2:1359906/113‑1 (MQ=255)

                                                    gCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGc                                                                                                >  1:1359906/1‑113 (MQ=255)

                                                    gCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATAc                                                                      >  2:472549/1‑139 (MQ=255)

                                                    gCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATAc                                                                      >  1:131435/1‑139 (MQ=255)

                                                          ctcACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTttc                                                                <  1:164823/139‑1 (MQ=255)

                                                            cACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTttctt                                                              <  2:733444/139‑1 (MQ=255)

                                                              cTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCg                                                                                 >  2:1164507/1‑118 (MQ=255)

                                                              cTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCg                                                                                 <  1:1164507/118‑1 (MQ=255)

                                                                ggCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTtcttctct                                                          >  2:1003403/1‑139 (MQ=255)

                                                                   aTTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTAc                                                                                                      >  1:473988/1‑92 (MQ=255)

                                                                   aTTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTAc                                                                                                      <  2:473988/92‑1 (MQ=255)

                                                                   aTTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCa                                                       >  1:845525/1‑139 (MQ=255)

                                                                                           tACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGAt                                                                                          >  2:362738/1‑80 (MQ=255)

                                                                                           tACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGAt                                                                                          <  1:362738/80‑1 (MQ=255)

                                                                                                cATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGt                          >  1:40836/1‑139 (MQ=255)

                                                                                                     ggTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATCCCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTtctc                     >  1:918529/1‑139 (MQ=255)

                                                                                                     ggTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTg                                                                                                                 <  1:572397/47‑1 (MQ=255)

                                                                                                     ggTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTg                                                                                                                 >  2:572397/1‑47 (MQ=255)

                                                                                                     ggTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTtctc                     >  1:858325/1‑139 (MQ=255)

                                                                                                     ggTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTtctc                     >  1:1271261/1‑139 (MQ=255)

                                                                                                     ggTTTTGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTtctc                     >  1:168950/1‑139 (MQ=255)

                                                                                                          tGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTTCTCTTAAc                >  1:537016/1‑139 (MQ=255)

                                                                                                          tGCGGCACTACTGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTTCTCTTAAc                <  2:40836/139‑1 (MQ=255)

                                                                                                                    ctGGTCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTTCTCTTAACGCCTTTTCta      <  1:472549/139‑1 (MQ=255)

                                                                                                                        tCGGGAACGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTTCTCTTAACGCCTTTTCtaataa  >  2:935020/1‑139 (MQ=255)

                                                                                                                               cGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTta                                                 <  2:564600/85‑1 (MQ=255)

                                                                                                                               cGGATTGGTGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTta                                                 >  1:564600/1‑85 (MQ=255)

CATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAATAAATCGAGCCTGTCTCACTGGCATTTTTCTCTTCATTTTTGACCAGTACAGCATCAGGTTTTGCGGCACTACTGGTCGGGAACGGATTGGCGGCATACCCTTGATCATTCGTACTTACGCTACGATTCACCGTCGCTGGCGTATACTTTTTCTTCTCTTCATCTTTATACTTTTTGAGTTCGCTTTGCGTTTCTCTTAACGCCTTTTCTAATAA  >  NC_000913/3901857‑3902115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A