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
A8 F1 I2 R1 765 53.2 2691310 93.4% 2513683 103.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,494,950 T→C Y85H (TAT→CAT)  ypdI → putative lipoprotein involved in colanic acid biosynthesis

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,494,9500TC100.0% 200.0 / NA 55Y85H (TAT→CAT) ypdIputative lipoprotein involved in colanic acid biosynthesis
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (28/27);  total (28/27)

AAACATCAGCGATGACGACCACACACTCTACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATTATCTTATTCATCCTGTGCGATAGCGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCACTACCGCCTGCC  >  NC_000913/2494816‑2495061
                                                                                                                                      |                                                                                                               
aaaCATCAGCGATGACGACCACACACTCTACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCt                                                                                                             <  1:1292650/139‑1 (MQ=255)
              acgacCACACACTCTACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGc                                                                                               >  1:1298007/1‑139 (MQ=255)
                 acCACACACTCTACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGAt                                                                                            >  1:271621/1‑139 (MQ=255)
                     cacacTCTACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTCATTCATCCTGTGCGATAACg                                                                                        >  2:659194/1‑139 (MQ=255)
                            tACAAAACTTCAGTCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTca                                                                                 >  2:334207/1‑139 (MQ=255)
                                    ttCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                         <  2:640722/139‑1 (MQ=255)
                                    ttCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                         >  2:1334004/1‑139 (MQ=255)
                                           aTCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCCCAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACa                                                                  <  2:330271/139‑1 (MQ=255)
                                              acaGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATc                                                               <  2:677479/139‑1 (MQ=255)
                                              acaGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATc                                                               <  1:781740/139‑1 (MQ=255)
                                                     aTTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGaa                                                                    >  1:103030/1‑127 (MQ=255)
                                                     aTTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGaa                                                                    <  2:103030/127‑1 (MQ=255)
                                                          gTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgct                                                   <  2:1298007/139‑1 (MQ=255)
                                                              aaGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACAt                                                                              >  2:747107/1‑108 (MQ=255)
                                                              aaGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACAt                                                                              <  1:747107/108‑1 (MQ=255)
                                                                gATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATa                                                                                           <  1:1099991/93‑1 (MQ=255)
                                                                gATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATa                                                                                           >  2:1099991/1‑93 (MQ=255)
                                                                gATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                         <  2:1220279/111‑1 (MQ=255)
                                                                gATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                         >  1:1220279/1‑111 (MQ=255)
                                                                     gagaAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAacac                                        <  1:1334004/139‑1 (MQ=255)
                                                                           aTGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCAt                                                                                                               >  1:1188348/1‑62 (MQ=255)
                                                                           aTGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgct                                                   >  1:1158276/1‑122 (MQ=255)
                                                                           aTGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgct                                                   <  2:1158276/122‑1 (MQ=255)
                                                                           aTGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGccc                                  >  2:767714/1‑139 (MQ=255)
                                                                             gcgcCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCaa                                <  2:271621/139‑1 (MQ=255)
                                                                             gcgcCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCaa                                <  1:334207/139‑1 (MQ=255)
                                                                                        aaaCCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATcc                     <  1:1033183/139‑1 (MQ=255)
                                                                                            cTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGAc                 <  1:767714/139‑1 (MQ=255)
                                                                                              cacaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                         <  1:1320016/81‑1 (MQ=255)
                                                                                              cacaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAg                                                                         >  2:1320016/1‑81 (MQ=255)
                                                                                              cacaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAg                           >  2:836799/1‑127 (MQ=255)
                                                                                              cacaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGAccc               >  2:435558/1‑139 (MQ=255)
                                                                                              cacaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGAccc               >  1:1150949/1‑139 (MQ=255)
                                                                                              cacaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGAGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAg                           <  1:836799/127‑1 (MQ=255)
                                                                                               acaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCAt                                                                                                               <  2:544922/42‑1 (MQ=255)
                                                                                               acaGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATCAt                                                                                                               >  1:544922/1‑42 (MQ=255)
                                                                                                 agaagaAATGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCatt            >  2:1179185/1‑137 (MQ=255)
                                                                                                      aaaTGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTTATCCTGTGCGATAACGTc                                                                                      <  2:748253/60‑1 (MQ=255)
                                                                                                      aaaTGCCGCCCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTc                                                                                      >  1:748253/1‑60 (MQ=255)
                                                                                                           ccgccCCCTTTTCCGACAAAGGCGAGTCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGcc  >  1:1111175/1‑139 (MQ=255)
                                                                                                           ccgccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATaac                                                                                         >  2:462753/1‑50 (MQ=255)
                                                                                                           ccgccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATaac                                                                                         <  1:462753/52‑3 (MQ=255)
                                                                                                           ccgccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCATTACCGCCTGcc  >  1:1284143/1‑139 (MQ=255)
                                                                                                             gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAg                           <  2:428824/112‑1 (MQ=255)
                                                                                                             gccCCCTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAg                           >  1:428824/1‑112 (MQ=255)
                                                                                                               ccccTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAacac                                        >  2:793904/1‑97 (MQ=255)
                                                                                                               ccccTTTTCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAacac                                        <  1:793904/97‑1 (MQ=255)
                                                                                                                   ttttCCGACAAAGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGaa                                                                    <  1:902678/65‑1 (MQ=255)
                                                                                                                   ttttCCGACAAAGCCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGaa                                                                    >  2:902678/1‑65 (MQ=255)
                                                                                                                             aaGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGc                                                                           <  2:102025/48‑1 (MQ=38)
                                                                                                                             aaGGCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGc                                                                           >  1:102025/1‑48 (MQ=38)
                                                                                                                               ggCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgctg                                                  >  1:884397/1‑71 (MQ=255)
                                                                                                                               ggCGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGTGAACAATCATGTctgatgctg                                                  <  2:884397/71‑1 (MQ=255)
                                                                                                                                 cGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGt                                                                       >  2:666015/1‑48 (MQ=38)
                                                                                                                                 cGAATCATCTTATTCATCCTGTGCGATAACGTCTTTCACATGGCAGGt                                                                       <  1:666015/48‑1 (MQ=38)
                                                                                                                                      |                                                                                                               
AAACATCAGCGATGACGACCACACACTCTACAAAACTTCAGCCATCACAGGCGATTTTGTTTAAGATGAGAGAAGATGCGCCACCATTAAACCTCACAGAAGAAATGCCGCCCCCTTTTCCGACAAAGGCGAATTATCTTATTCATCCTGTGCGATAGCGTCTTTCACATGGCAGGTGAACAATCATGTCTGATGCTGATGTGAACACCTGCCCAAATGAGCCATCCTGACCCACTACCGCCTGCC  >  NC_000913/2494816‑2495061

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A