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	2,277,619	G→C	23.8%	A377G (GCA→GGA)	btuB ←	vitamin B12/cobalamin outer membrane transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,277,619	0	G	C	23.8%	84.8 / 24.6	55	A377G (GCA→GGA)	btuB	vitamin B12/cobalamin outer membrane transporter
Reads supporting (aligned to +/- strand): ref base G (30/11); new base C (7/6); total (38/17)
Fisher's exact test for biased strand distribution p-value = 3.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCGGTATTACG  >  minE/2277581‑2277683

ttCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACtt                                    <  1:835398/69‑1 (MQ=255)

 tCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACttg                                   >  1:1716949/1‑69 (MQ=255)

 tCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACtt                                    <  1:361020/68‑1 (MQ=255)

       acgacCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAg                             >  1:2220327/1‑69 (MQ=255)

        cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg                             >  1:1140641/1‑68 (MQ=255)

        cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg                             >  1:2652026/1‑68 (MQ=255)

        cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg                             >  1:358266/1‑68 (MQ=255)

        cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg                             >  1:442789/1‑68 (MQ=255)

        cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg                             >  1:1898742/1‑68 (MQ=255)

        cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTCGCTGCAg                             >  1:387305/1‑68 (MQ=255)

        cgacCAAACTGAGAATTATCGTCGCAGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg                             >  1:861381/1‑68 (MQ=255)

               aCTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     <  1:323795/69‑1 (MQ=255)

               aCTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     <  1:1543739/69‑1 (MQ=255)

               aCTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     <  1:416026/69‑1 (MQ=255)

                 tgtgAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCaga                   <  1:1835946/69‑1 (MQ=255)

                 tgtgAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCaga                   <  1:3300946/69‑1 (MQ=255)

                 tgtgAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCaga                   <  1:1669890/69‑1 (MQ=255)

                     aGTTATCGTCACTGCTTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCagata                 <  1:2651043/67‑1 (MQ=255)

                     aGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCagataga               >  1:2376560/1‑69 (MQ=255)

                     aGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCagataga               >  1:1108553/1‑69 (MQ=255)

                     aGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCagata                 <  1:2777580/67‑1 (MQ=255)

                      attATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAGCCCAGTCagatagat              <  1:1826605/68‑1 (MQ=255)

                      attATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAGCCCAGTCagatagat              <  1:1990297/68‑1 (MQ=255)

                      attATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAGCCCAGTCagatagat              <  1:1994254/68‑1 (MQ=255)

                      attATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAGCCCAGTCagatagat              <  1:448117/68‑1 (MQ=255)

                      attATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAGCCCAGTCagatagat              <  1:2314032/68‑1 (MQ=255)

                      attATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAGCCCAGTCagatagat              <  1:1743977/68‑1 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTTAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:1224645/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     >  1:1307019/1‑59 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     >  1:2820658/1‑59 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     >  1:2971345/1‑59 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     >  1:331614/1‑59 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     >  1:3329377/1‑59 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa                     >  1:1497401/1‑59 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATGGATGcc           >  1:1805626/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:447381/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:385943/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:963159/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:2783055/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:2764923/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:1087534/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:2651802/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:2566580/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:2409963/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:1765728/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:1287081/1‑69 (MQ=255)

                         aTCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:1364270/1‑69 (MQ=255)

                         aTCGTCACTGCGTACTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGcc           >  1:28792/1‑69 (MQ=255)

                            gTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCgg         <  1:1088309/68‑1 (MQ=255)

                            gTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCGGt        >  1:1008764/1‑69 (MQ=255)

                            gTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCGGt        >  1:59919/1‑69 (MQ=255)

                            gTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCGGt        >  1:2039455/1‑69 (MQ=255)

                            gTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCGGt        >  1:2892193/1‑69 (MQ=255)

                                   cGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCGGTATTACg  >  1:501596/1‑68 (MQ=255)

                                   cGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCGGTATTACg  >  1:671523/1‑68 (MQ=255)

                                     tgctgcGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCTGTCagataga               >  1:1042312/1‑53 (MQ=255)

                                     tgctgcGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCagataga               >  1:2663400/1‑53 (MQ=255)

                                     tgctgcGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCagatag                >  1:2695397/1‑52 (MQ=255)

                                     tgctgcGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCaga                   >  1:1720942/1‑49 (MQ=255)

TTCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGATAGATGCCGGTATTACG  >  minE/2277581‑2277683

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A