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
A1 F3 I0 R2	260	44.3	3360226	90.5%	3041004	64.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,793,630	G→A	25.4%	S35S (TCC→TCT)	ydiV ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,793,630	0	G	A	25.4%	116.4 / 40.2	67	S35S (TCC→TCT)	ydiV	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (39/11); new base A (5/12); total (44/23)
Fisher's exact test for biased strand distribution p-value = 6.89e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.50e-01

ATGTTGCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTATCGGCAGGAAATAG  >  W3110S.gb/1793564‑1793696

aTGTTTCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGgaga                                                                <  1:2268081/71‑1 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:2868713/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:1968092/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:2067674/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:3054431/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:1729527/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:564655/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:611403/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:770541/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:945044/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:2398223/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:2457685/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:247119/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:2490446/1‑68 (MQ=255)

     gCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGaaa                                                              >  1:2690156/1‑68 (MQ=255)

         ctcGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATggt                                                          <  1:442929/68‑2 (MQ=255)

         ctcGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATggg                                                          <  1:2222865/68‑1 (MQ=255)

            ggTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAAtt                                                     >  1:959067/1‑70 (MQ=255)

            ggTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAAtt                                                     >  1:3249934/1‑70 (MQ=255)

            ggTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAAtt                                                     >  1:2154532/1‑70 (MQ=255)

            ggTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAAtt                                                     >  1:3298418/1‑70 (MQ=255)

            ggTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAAtt                                                     >  1:1687142/1‑70 (MQ=255)

            ggTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACAATCTTCACTGGAGAAATGGGTAAtt                                                     >  1:418995/1‑70 (MQ=255)

                            acacGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGc                                           >  1:2997946/4‑64 (MQ=255)

                            aCCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGt                                                         >  1:950746/1‑50 (MQ=255)

                            aCCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAAt                                                      >  1:1881158/1‑53 (MQ=255)

                            aCCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGc                                           >  1:1885066/1‑64 (MQ=255)

                            aCCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGc                                           >  1:1478808/1‑64 (MQ=255)

                            aCCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGc                                           >  1:2782641/1‑64 (MQ=255)

                            aCCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGc                                           >  1:1183454/1‑64 (MQ=255)

                                gACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACt                                >  1:1110977/1‑71 (MQ=255)

                                gACTCGTCGGGATACGAACCGAACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGAc                                       >  1:1202661/1‑64 (MQ=255)

                                           aTACGAACCGTACCATCTTCACTGGAGAAATGGGTAAtt                                                     >  1:946818/1‑39 (MQ=255)

                                           aTACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCaa                                              >  1:1049525/1‑46 (MQ=255)

                                           aTACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCaa                                              >  1:2185309/1‑46 (MQ=255)

                                              cGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTctct                  >  1:1114482/1‑71 (MQ=255)

                                               gAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:804784/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:3336052/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:326741/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:22098/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:2729317/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:1032026/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:1122655/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:555794/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:407262/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:3146651/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:2244287/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:2733167/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:2901584/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:2762767/71‑1 (MQ=255)

                                               gAACCGTACCATCTTCACTAGACAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:805145/71‑1 (MQ=255)

                                                aaCCGTACCATCTTCACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCtt                 <  1:1849583/70‑1 (MQ=255)

                                                            ttCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTAt               >  1:2804511/1‑60 (MQ=255)

                                                            ttCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTAt               >  1:2351159/1‑60 (MQ=255)

                                                            ttCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTAt               >  1:1222816/1‑60 (MQ=255)

                                                            ttCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTAt               >  1:529034/1‑60 (MQ=255)

                                                            ttCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTAt               >  1:1737546/1‑60 (MQ=255)

                                                            ttCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTATCGGCAGGaaa     >  1:2922224/1‑70 (MQ=255)

                                                              cACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTATCGGCAGGAAATAg  >  1:3116756/1‑71 (MQ=255)

                                                              cACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTATCGGCAGGAAATAg  >  1:150545/1‑71 (MQ=255)

                                                              cACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTATCGGCAGGAAATAg  >  1:787540/1‑71 (MQ=255)

                                                              cACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTATCGGCAGGAAATAg  >  1:1926140/1‑71 (MQ=255)

                                                              cACTAGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTATCGGCAGGAAATAg  >  1:2568778/1‑71 (MQ=255)

                                                                 tGGAGAAATGGGTAATTAACTCAACGCCGACAAgg                                   <  1:1426384/35‑1 (MQ=255)

                                                                 tGGAGAAATGGGTAATTAACTCAACGCCGACAAgg                                   <  1:2858526/35‑1 (MQ=255)

                                                                 tGGAGAAATGGGTAATTAACTCAACGCCGACAAgg                                   <  1:2261597/35‑1 (MQ=255)

                                                                 tGGAGAAATGGGTAATTAACTCAACGCCGACAAgg                                   <  1:1186771/35‑1 (MQ=255)

ATGTTGCTCCTCGGTAAGTTGCGCTATAACCCGACTCGTCGGGATACGAACCGTACCATCTTCACTGGAGAAATGGGTAATTAACTCAACGCCGACAAGGACTTGCTGGTTGTCTCTTATCGGCAGGAAATAG  >  W3110S.gb/1793564‑1793696

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A