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
A4 F60 I1 R1	18	54.8	1909210	98.2%	1874844	138.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,883	+C	coding (667/687 nt)	rph ←	truncated RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,879	1	.	C	91.4%	115.8 / 3.9	35	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand): ref base . (1/2); new base C (14/18); total (15/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑CCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGA  >  NC_000913/3815748‑3816009

cTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑ccccctcg                                                                                                                             >  1:89170/1‑136 (MQ=255)

    cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGcc                                                                                                                         <  1:64669/140‑1 (MQ=255)

           atGGTTTCATGCCTTAGCTCCTCATGTTACTTTTCTAGAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCca                                                                                                                  <  1:377405/140‑1 (MQ=255)

                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATg                                                                                                          >  1:900966/1‑140 (MQ=255)

                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATg                                                                                                          >  1:192079/1‑140 (MQ=255)

                      ccTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACACATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGt                                                                                                       <  2:618557/140‑1 (MQ=255)

                        ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  1:134596/140‑1 (MQ=255)

                        ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     >  1:803298/1‑140 (MQ=255)

                        ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  1:592948/140‑1 (MQ=255)

                        ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  2:701829/140‑1 (MQ=255)

                         tccctcctcATCTTTCTTCTCTACAAACAAAAAAAAGGCGACTCAACAGTCCGCTTAAAAATCAAGTTGCCAGCGCCGGCTTCTGCCGCGCTACAAAGGATTCGA‑TTCCCCC‑TCCGGCCAGAGCCAACAAGATGAGTAGc                                                                                                    <  2:2588/137‑1 (MQ=255)

                         tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTAGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCca                                                                                                                  <  2:807090/126‑1 (MQ=255)

                         tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTAGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCca                                                                                                                  >  1:807090/1‑126 (MQ=255)

                         tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCAACAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     >  1:237412/1‑139 (MQ=255)

                         tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCAACAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  2:237412/139‑1 (MQ=255)

                             tcctcATCTTACTTTTCAACAGCCAAAAAAAAGGCCACTTATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                                <  2:399502/140‑1 (MQ=255)

                                       aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCGAACTAGATGAGTATCTCTTCATGGGTGaa                                                                                      >  1:399502/1‑140 (MQ=255)

                                       aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑CCCCTTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                      >  1:683641/1‑140 (MQ=255)

                                           ttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                                                                                  <  2:192079/140‑1 (MQ=255)

                                            tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCt                                                                                 >  2:495143/1‑140 (MQ=255)

                                              tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGGCAACAAGGTGAGTAACTCTTCGTGGGTGAACGGCTCg                                                                               >  1:281074/1‑140 (MQ=255)

                                                       aaaaaaGGCGCCTCATCAGTCGTCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGTACGGCTCGCCTTCTGcc                                                                      >  2:186661/1‑140 (MQ=255)

                                                               ggACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              <  2:89170/139‑1 (MQ=255)

                                                               cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              >  1:587327/1‑140 (MQ=255)

                                                               cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCACTTCATGGGTGTACTGCTCGCATTCTGCCGTCCCCTg                                                              >  1:395560/1‑140 (MQ=255)

                                                               cGACTCATCAGTCGCCTCAAAAATCAGTTTGGCAGCGCCACCTTCTGCTTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              <  2:395560/140‑1 (MQ=255)

                                                                            gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              >  1:142227/1‑127 (MQ=255)

                                                                            gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              <  2:142227/127‑1 (MQ=255)

                                                                            gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                 >  1:606671/1‑140 (MQ=255)

                                                                            gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                 >  2:919885/1‑140 (MQ=255)

                                                                               ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                              >  1:727123/1‑140 (MQ=255)

                                                                                        aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                     <  2:659574/140‑1 (MQ=255)

                                                                                         gTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg                                    <  1:495143/140‑1 (MQ=255)

                                                                                                 gcgcCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                            <  2:727123/140‑1 (MQ=255)

                                                                                                 gcgcCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                            <  2:900966/140‑1 (MQ=255)

                                                                                                 gcgcCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑CCCCTTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                            <  2:683641/140‑1 (MQ=255)

                                                                                                                 cGCTACAATGGATTCGA‑TTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGTACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct            <  1:186661/140‑1 (MQ=255)

                                                                                                                         tGGATTCGACTC‑CCCC‑TCGGGCCAGAGCCATCAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa    <  1:590091/140‑1 (MQ=255)

                                                                                                                           gattcga‑ttcCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga  <  2:893696/140‑1 (MQ=255)

CTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑CCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGA  >  NC_000913/3815748‑3816009

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A