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	2,756,465	T→A	33.7%	I118I (ATA→ATT)	rsmB ←	16S rRNA m5C967 methyltransferase, S‑adenosyl‑L‑methionine‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,756,465	0	T	A	33.7%	90.3 / 71.1	92	I118I (ATA→ATT)	rsmB	16S rRNA m5C967 methyltransferase, S‑adenosyl‑L‑methionine‑dependent
Reads supporting (aligned to +/- strand): ref base T (40/21); new base A (17/14); total (57/35)
Fisher's exact test for biased strand distribution p-value = 3.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

ACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTCAGCCAGCGC  >  minE/2756402‑2756527

aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACGGTTTATc                                                             >  1:1387994/1‑67 (MQ=255)

aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATc                                                             >  1:3266021/1‑67 (MQ=255)

aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                                                           >  1:962769/1‑69 (MQ=255)

aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                                                           >  1:2660656/1‑69 (MQ=255)

aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                                                           >  1:1268645/1‑69 (MQ=255)

aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCa                                                            >  1:3291579/1‑68 (MQ=255)

aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTATATc                                                             >  1:3317353/1‑67 (MQ=255)

      aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                                      <  1:1294275/68‑3 (MQ=255)

      aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                                      <  1:2122120/68‑3 (MQ=255)

      aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                                      <  1:202323/68‑3 (MQ=255)

      aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                                      <  1:3213334/68‑3 (MQ=255)

      aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                                      <  1:867393/68‑3 (MQ=255)

      aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                                      <  1:3146924/68‑3 (MQ=255)

      aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                                      <  1:970101/68‑3 (MQ=255)

         aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTa                                                               >  1:2161071/1‑56 (MQ=255)

         aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                                                  >  1:1771175/1‑69 (MQ=255)

         aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                                                  >  1:2011646/1‑69 (MQ=255)

         aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                                                  >  1:3272867/1‑69 (MQ=255)

         aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                                                  >  1:394218/1‑69 (MQ=255)

         aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                                                  >  1:2900158/1‑69 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:2175184/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:2936825/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:2216327/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:2811800/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:2513501/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:1887824/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:2284221/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:3116577/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:3261252/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:1588931/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:500621/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:596296/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:1332157/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:862744/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:90237/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:1133030/1‑53 (MQ=255)

               ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                                            >  1:919592/1‑53 (MQ=255)

                       aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGAc                                          >  1:1684916/1‑63 (MQ=255)

                       aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa                                    >  1:3057908/1‑69 (MQ=255)

                       aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa                                    >  1:3157356/1‑69 (MQ=255)

                       aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa                                    >  1:3054266/1‑69 (MQ=255)

                       aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa                                    >  1:593708/1‑69 (MQ=255)

                       aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa                                    >  1:1037296/1‑69 (MQ=255)

                       aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa                                    >  1:1699742/1‑69 (MQ=255)

                       aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa                                    >  1:2109202/1‑69 (MQ=255)

                       aCTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                                      <  1:1363903/51‑3 (MQ=255)

                             cttGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:227503/67‑1 (MQ=255)

                             cttGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:1023512/67‑1 (MQ=255)

                             cttGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:476676/67‑1 (MQ=255)

                             cttGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:2492605/67‑1 (MQ=255)

                                   gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt                                   <  1:2209479/58‑1 (MQ=255)

                                   gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt                                   <  1:1655114/58‑1 (MQ=255)

                                   gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt                                   <  1:1676372/58‑1 (MQ=255)

                                   gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt                                   <  1:1429955/58‑1 (MQ=255)

                                   gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt                                   <  1:606395/58‑1 (MQ=255)

                                   gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt                                   <  1:1198911/58‑1 (MQ=255)

                                      gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCTATAGCGcc                       <  1:3401015/67‑1 (MQ=255)

                                      gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGcc                       <  1:532771/67‑1 (MQ=255)

                                      gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGcc                       <  1:808027/67‑1 (MQ=255)

                                      gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGcc                       <  1:317264/67‑1 (MQ=255)

                                      gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGcc                       <  1:1609955/67‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACTCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     <  1:564367/68‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                >  1:2301424/1‑41 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                >  1:1275247/1‑41 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:904104/41‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                >  1:1093742/1‑41 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                >  1:471732/1‑41 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:1080820/41‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:1496447/41‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                >  1:1538745/1‑41 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                >  1:1673484/1‑41 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                >  1:3203345/1‑41 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:241712/41‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:2236155/41‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:2744949/41‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc                                <  1:2777855/41‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     <  1:1578717/68‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     <  1:3278586/68‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     <  1:167603/68‑1 (MQ=255)

                                                       acacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     <  1:2562018/68‑1 (MQ=255)

                                                       acacCGTTTATCAA‑CCTTTAAGTTGCGGACGCTTAATTGc                                >  1:659244/1‑40 (MQ=39)

                                                       acacCGTTTATAAACCCTTTAAGTTGCGGACGCTTAATTg                                 >  1:2330670/1‑40 (MQ=255)

                                                        cacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     >  1:2223482/1‑67 (MQ=255)

                                                        cacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     >  1:68508/1‑67 (MQ=255)

                                                        cacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     >  1:2852746/1‑67 (MQ=255)

                                                        cacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     >  1:1293409/1‑67 (MQ=255)

                                                        cacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     >  1:2227417/1‑67 (MQ=255)

                                                        cacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     >  1:2199691/1‑67 (MQ=255)

                                                        cacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     >  1:1450301/1‑67 (MQ=255)

                                                        cacCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagcaag     >  1:514540/1‑67 (MQ=255)

                                                          ccGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTCAGCCAgcgc  >  1:2449093/1‑68 (MQ=255)

                                                          ccGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTCAGCCAgcgc  >  1:1826515/1‑68 (MQ=255)

                                                              ttATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTcagccag     <  1:1395449/61‑1 (MQ=255)

ACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCCTTCAACCGTTTCAGCCAGCGC  >  minE/2756402‑2756527

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